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Baker IR, Matzen SL, Schuler CJ, Toner BM, Girguis PR. Aerobic iron-oxidizing bacteria secrete metabolites that markedly impede abiotic iron oxidation. PNAS NEXUS 2023; 2:pgad421. [PMID: 38111821 PMCID: PMC10727123 DOI: 10.1093/pnasnexus/pgad421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 11/29/2023] [Indexed: 12/20/2023]
Abstract
Iron is one of the Earth's most abundant elements and is required for essentially all forms of life. Yet, iron's reactivity with oxygen and poor solubility in its oxidized form (Fe3+) mean that it is often a limiting nutrient in oxic, near-neutral pH environments like Earth's ocean. In addition to being a vital nutrient, there is a diversity of aerobic organisms that oxidize ferrous iron (Fe2+) to harness energy for growth and biosynthesis. Accordingly, these organisms rely on access to co-existing Fe2+ and O2 to survive. It is generally presumed that such aerobic iron-oxidizing bacteria (FeOB) are relegated to low-oxygen regimes where abiotic iron oxidation rates are slower, yet some FeOB live in higher oxygen environments where they cannot rely on lower oxygen concentrations to overcome abiotic competition. We hypothesized that FeOB chemically alter their environment to limit abiotic interactions between Fe2+ and O2. To test this, we incubated the secreted metabolites (collectively known as the exometabolome) of the deep-sea iron- and hydrogen-oxidizing bacterium Ghiorsea bivora TAG-1 with ferrous iron and oxygen. We found that this FeOB's iron-oxidizing exometabolome markedly impedes the abiotic oxidation of ferrous iron, increasing the half-life of Fe2+ 100-fold from ∼3 to ∼335 days in the presence of O2, while the exometabolome of TAG-1 grown on hydrogen had no effect. Moreover, the few precipitates that formed in the presence of TAG-1's iron-oxidizing exometabolome were poorly crystalline, compared with the abundant iron particles that mineralized in the absence of abiotic controls. We offer an initial exploration of TAG-1's iron-oxidizing exometabolome and discuss potential key contributors to this process. Overall, our findings demonstrate that the exometabolome as a whole leads to a sustained accumulation of ferrous iron in the presence of oxygen, consequently altering the redox equilibrium. This previously unknown adaptation likely enables these microorganisms to persist in an iron-oxidizing and iron-precipitating world and could have impacts on the bioavailability of iron to FeOB and other life in iron-limiting environments.
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Affiliation(s)
- Isabel R Baker
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Sarick L Matzen
- Department of Soil, Water, and Climate, University of Minnesota Twin Cities, Saint Paul, MN 55108, USA
| | - Christopher J Schuler
- Department of Earth and Environmental Sciences, University of Minnesota Twin Cities, Saint Paul, MN 55108, USA
| | - Brandy M Toner
- Department of Soil, Water, and Climate, University of Minnesota Twin Cities, Saint Paul, MN 55108, USA
- Department of Earth and Environmental Sciences, University of Minnesota Twin Cities, Saint Paul, MN 55108, USA
| | - Peter R Girguis
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
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Yang H, Lu L, Chen Y, Ye J. Transcriptomic Analysis Reveals the Response of the Bacterium Priestia Aryabhattai SK1-7 to Interactions and Dissolution with Potassium Feldspar. Appl Environ Microbiol 2023; 89:e0203422. [PMID: 37154709 DOI: 10.1128/aem.02034-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023] Open
Abstract
Potassium feldspar (K2O·Al2O3·6SiO2) is considered to be the most important source of potash fertilizer. The use of microorganisms to dissolve potassium feldspar is a low-cost and environmentally friendly method. Priestia aryabhattai SK1-7 is a strain with a strong ability to dissolve potassium feldspar; it showed a faster pH drop and produced more acid in the medium with potassium feldspar as the insoluble potassium source than in the medium with K2HPO4 as the soluble potassium source. We speculated whether the cause of acid production was related to one or more stresses, such as mineral-induced generation of reactive oxygen species (ROS), the presence of aluminum in potassium feldspar, and cell membrane damage due to friction between SK1-7 and potassium feldspar, and analyzed it by transcriptome. The results revealed that the expression of the genes related to pyruvate metabolism, the two-component system, DNA repair, and oxidative stress pathways in strain SK1-7 was significantly upregulated in potassium feldspar medium. The subsequent validation experiments revealed that ROS were the stress faced by strain SK1-7 when interacting with potassium feldspar and led to a decrease in the total fatty acid content of SK1-7. In the face of ROS stress, strain SK1-7 upregulated the expression of the maeA-1 gene, allowing malic enzyme (ME2) to produce more pyruvate to be secreted outside the cell using malate as a substrate. Pyruvate is both a scavenger of external ROS and a gas pedal of dissolved potassium feldspar. IMPORTANCE Mineral-microbe interactions play important roles in the biogeochemical cycling of elements. Manipulating mineral-microbe interactions and optimizing the consequences of such interactions can be used to benefit society. It is necessary to explore the black hole of the mechanism of interaction between the two. In this study, it is revealed that P. aryabhattai SK1-7 faces mineral-induced ROS stress by upregulating a series of antioxidant genes as a passive defense, while overexpression of malic enzyme (ME2) secretes pyruvate to scavenge ROS as well as to increase feldspar dissolution, releasing K, Al, and Si into the medium. Our research provides a theoretical basis for improving the ability of microorganisms to weather minerals through genetic manipulation in the future.
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Affiliation(s)
- Hui Yang
- College of Forestry and Co-Innovation Center for Sustainable Forestry in Southern China, Jiangsu Key Laboratory for Prevention and Management of Invasive Species, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Lanxiang Lu
- College of Forestry and Co-Innovation Center for Sustainable Forestry in Southern China, Jiangsu Key Laboratory for Prevention and Management of Invasive Species, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Yifan Chen
- College of Forestry and Co-Innovation Center for Sustainable Forestry in Southern China, Jiangsu Key Laboratory for Prevention and Management of Invasive Species, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Jianren Ye
- College of Forestry and Co-Innovation Center for Sustainable Forestry in Southern China, Jiangsu Key Laboratory for Prevention and Management of Invasive Species, Nanjing Forestry University, Nanjing, Jiangsu, China
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Sindhu SS, Sehrawat A, Glick BR. The involvement of organic acids in soil fertility, plant health and environment sustainability. Arch Microbiol 2022; 204:720. [DOI: 10.1007/s00203-022-03321-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 10/22/2022] [Accepted: 11/03/2022] [Indexed: 11/21/2022]
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A miniaturized bionic ocean-battery mimicking the structure of marine microbial ecosystems. Nat Commun 2022; 13:5608. [PMID: 36153325 PMCID: PMC9509365 DOI: 10.1038/s41467-022-33358-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 09/14/2022] [Indexed: 11/08/2022] Open
Abstract
AbstractMarine microbial ecosystems can be viewed as a huge ocean-battery charged by solar energy. It provides a model for fabricating bio-solar cell, a bioelectrochemical system that converts light into electricity. Here, we fabricate a bio-solar cell consisting of a four-species microbial community by mimicking the ecological structure of marine microbial ecosystems. We demonstrate such ecological structure consisting of primary producer, primary degrader, and ultimate consumers is essential for achieving high power density and stability. Furthermore, the four-species microbial community is assembled into a spatial-temporally compacted cell using conductive hydrogel as a sediment-like anaerobic matrix, forming a miniaturized bionic ocean-battery. This battery directly converts light into electricity with a maximum power of 380 μW and stably operates for over one month. Reproducing the photoelectric conversion function of marine microbial ecosystems in this bionic battery overcomes the sluggish and network-like electron transfer, showing the biotechnological potential of synthetic microbial ecology.
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Suhadolnik MLS, Costa PS, Castro GM, Lobo FP, Nascimento AMA. Comprehensive insights into arsenic- and iron-redox genes, their taxonomy and associated environmental drivers deciphered by a meta-analysis. ENVIRONMENT INTERNATIONAL 2021; 146:106234. [PMID: 33181412 DOI: 10.1016/j.envint.2020.106234] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 09/23/2020] [Accepted: 10/20/2020] [Indexed: 06/11/2023]
Abstract
In nature, arsenic (As) and iron (Fe) biotransformation are interconnected, influencing local As mobility and toxicity. While As- or Fe-metabolizing microorganisms are widely documented, knowledge concerning their cycling genes, associated with geophysicochemical data and taxonomic distribution, remains scarce. We performed a meta-analysis to explore the distribution and environmental importance of As- and Fe-redox genes (AsRGs and FeRGs) and predict their significant correlations and hosts. The most abundant and ubiquitous AsRGs and FeRGs were arsC and ccoN, respectively. The ccoN gene had the highest frequency at pH ≥ 9.1, in which dissolved Fe(II) is scarce, possibly contributing to enhanced host survival. Fe(III) oxidation genes iro and ccoN appear to be associated with As(V) detoxification in mesophilic environments. No correlation was observed between Fe(III) reduction gene omcB and arsenate reductase genes. Cytochromes with putative roles in Fe-redox reactions were identified (including yceJ and fbcH) and were significantly correlated with As(V) reduction genes under diverse geophysicochemical conditions. The taxonomies of AsRGs and FeRGs-carrying contigs revealed great diversity, among which various, such as Chlamydea (arsC) and Firmicutes (omcB), were previously undescribed. Nearly all (98.9%) of the AsRGs and FeRGs were not carried by any plasmid sequences. This meta-analysis expands our understanding of the global environmental, taxonomic and functional microbiome involved in As- and Fe-redox transformations. Moreover, these findings should help guide studies on putative in vivo functional roles of cytochromes in Fe-redox pathways.
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Affiliation(s)
- Maria Luíza S Suhadolnik
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Brazil
| | - Patrícia S Costa
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Brazil
| | - Giovanni M Castro
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Brazil
| | - Francisco P Lobo
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Brazil
| | - Andréa M A Nascimento
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Brazil.
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Liu Q, Liu B, Li W, Zhao X, Zuo W, Xing D. Impact of Ferrous Iron on Microbial Community of the Biofilm in Microbial Fuel Cells. Front Microbiol 2017. [PMID: 28638368 PMCID: PMC5461252 DOI: 10.3389/fmicb.2017.00920] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The performance of microbial electrochemical cells depends upon microbial community structure and metabolic activity of the electrode biofilms. Iron as a signal affects biofilm development and enrichment of exoelectrogenic bacteria. In this study, the effect of ferrous iron on microbial communities of the electrode biofilms in microbial fuel cells (MFCs) was investigated. Voltage production showed that ferrous iron of 100 μM facilitated MFC start-up compared to 150 μM, 200 μM, and without supplement of ferrous iron. However, higher concentration of ferrous iron had an inhibitive influence on current generation after 30 days of operation. Illumina Hiseq sequencing of 16S rRNA gene amplicons indicated that ferrous iron substantially changed microbial community structures of both anode and cathode biofilms. Principal component analysis showed that the response of microbial communities of the anode biofilms to higher concentration of ferrous iron was more sensitive. The majority of predominant populations of the anode biofilms in MFCs belonged to Geobacter, which was different from the populations of the cathode biofilms. An obvious shift of community structures of the cathode biofilms occurred after ferrous iron addition. This study implied that ferrous iron influenced the power output and microbial community of MFCs.
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Affiliation(s)
- Qian Liu
- State Key Laboratory of Urban Water Resource and Environment, School of Municipal and Environmental Engineering, Harbin Institute of TechnologyHarbin, China
| | - Bingfeng Liu
- State Key Laboratory of Urban Water Resource and Environment, School of Municipal and Environmental Engineering, Harbin Institute of TechnologyHarbin, China
| | - Wei Li
- State Key Laboratory of Urban Water Resource and Environment, School of Municipal and Environmental Engineering, Harbin Institute of TechnologyHarbin, China
| | - Xin Zhao
- State Key Laboratory of Urban Water Resource and Environment, School of Municipal and Environmental Engineering, Harbin Institute of TechnologyHarbin, China
| | - Wenjing Zuo
- State Key Laboratory of Urban Water Resource and Environment, School of Municipal and Environmental Engineering, Harbin Institute of TechnologyHarbin, China
| | - Defeng Xing
- State Key Laboratory of Urban Water Resource and Environment, School of Municipal and Environmental Engineering, Harbin Institute of TechnologyHarbin, China
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Plant-Microbiota Interactions as a Driver of the Mineral Turnover in the Rhizosphere. ADVANCES IN APPLIED MICROBIOLOGY 2016; 95:1-67. [PMID: 27261781 DOI: 10.1016/bs.aambs.2016.03.001] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
A major challenge facing agriculture in the 21st century is the need to increase the productivity of cultivated land while reducing the environmentally harmful consequences of mineral fertilization. The microorganisms thriving in association and interacting with plant roots, the plant microbiota, represent a potential resource of plant probiotic function, capable of conjugating crop productivity with sustainable management in agroecosystems. However, a limited knowledge of the organismal interactions occurring at the root-soil interface is currently hampering the development and use of beneficial plant-microbiota interactions in agriculture. Therefore, a comprehensive understanding of the recruitment cues of the plant microbiota and the molecular basis of nutrient turnover in the rhizosphere will be required to move toward efficient and sustainable crop nutrition. In this chapter, we will discuss recent insights into plant-microbiota interactions at the root-soil interface, illustrate the processes driving mineral dynamics in soil, and propose experimental avenues to further integrate the metabolic potential of the plant microbiota into crop management and breeding strategies for sustainable agricultural production.
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Wessels HJCT, de Almeida NM, Kartal B, Keltjens JT. Bacterial Electron Transfer Chains Primed by Proteomics. Adv Microb Physiol 2016; 68:219-352. [PMID: 27134025 DOI: 10.1016/bs.ampbs.2016.02.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Electron transport phosphorylation is the central mechanism for most prokaryotic species to harvest energy released in the respiration of their substrates as ATP. Microorganisms have evolved incredible variations on this principle, most of these we perhaps do not know, considering that only a fraction of the microbial richness is known. Besides these variations, microbial species may show substantial versatility in using respiratory systems. In connection herewith, regulatory mechanisms control the expression of these respiratory enzyme systems and their assembly at the translational and posttranslational levels, to optimally accommodate changes in the supply of their energy substrates. Here, we present an overview of methods and techniques from the field of proteomics to explore bacterial electron transfer chains and their regulation at levels ranging from the whole organism down to the Ångstrom scales of protein structures. From the survey of the literature on this subject, it is concluded that proteomics, indeed, has substantially contributed to our comprehending of bacterial respiratory mechanisms, often in elegant combinations with genetic and biochemical approaches. However, we also note that advanced proteomics offers a wealth of opportunities, which have not been exploited at all, or at best underexploited in hypothesis-driving and hypothesis-driven research on bacterial bioenergetics. Examples obtained from the related area of mitochondrial oxidative phosphorylation research, where the application of advanced proteomics is more common, may illustrate these opportunities.
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Affiliation(s)
- H J C T Wessels
- Nijmegen Center for Mitochondrial Disorders, Radboud Proteomics Centre, Translational Metabolic Laboratory, Radboud University Medical Center, Nijmegen, The Netherlands
| | - N M de Almeida
- Institute of Water and Wetland Research, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - B Kartal
- Institute of Water and Wetland Research, Radboud University Nijmegen, Nijmegen, The Netherlands; Laboratory of Microbiology, Ghent University, Ghent, Belgium
| | - J T Keltjens
- Institute of Water and Wetland Research, Radboud University Nijmegen, Nijmegen, The Netherlands.
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Distribution of microbial arsenic reduction, oxidation and extrusion genes along a wide range of environmental arsenic concentrations. PLoS One 2013; 8:e78890. [PMID: 24205341 PMCID: PMC3815024 DOI: 10.1371/journal.pone.0078890] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Accepted: 09/17/2013] [Indexed: 11/28/2022] Open
Abstract
The presence of the arsenic oxidation, reduction, and extrusion genes arsC, arrA, aioA, and acr3 was explored in a range of natural environments in northern Chile, with arsenic concentrations spanning six orders of magnitude. A combination of primers from the literature and newly designed primers were used to explore the presence of the arsC gene, coding for the reduction of As (V) to As (III) in one of the most common detoxification mechanisms. Enterobacterial related arsC genes appeared only in the environments with the lowest As concentration, while Firmicutes-like genes were present throughout the range of As concentrations. The arrA gene, involved in anaerobic respiration using As (V) as electron acceptor, was found in all the systems studied. The As (III) oxidation gene aioA and the As (III) transport gene acr3 were tracked with two primer sets each and they were also found to be spread through the As concentration gradient. Sediment samples had a higher number of arsenic related genes than water samples. Considering the results of the bacterial community composition available for these samples, the higher microbial phylogenetic diversity of microbes inhabiting the sediments may explain the increased number of genetic resources found to cope with arsenic. Overall, the environmental distribution of arsenic related genes suggests that the occurrence of different ArsC families provides different degrees of protection against arsenic as previously described in laboratory strains, and that the glutaredoxin (Grx)-linked arsenate reductases related to Enterobacteria do not confer enough arsenic resistance to live above certain levels of As concentrations.
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The genome of Pseudomonas fluorescens strain R124 demonstrates phenotypic adaptation to the mineral environment. J Bacteriol 2013; 195:4793-803. [PMID: 23995634 DOI: 10.1128/jb.00825-13] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Microbial adaptation to environmental conditions is a complex process, including acquisition of positive traits through horizontal gene transfer or the modification of existing genes through duplication and/or mutation. In this study, we examined the adaptation of a Pseudomonas fluorescens isolate (R124) from the nutrient-limited mineral environment of a silica cave in comparison with P. fluorescens isolates from surface soil and the rhizosphere. Examination of metal homeostasis gene pathways demonstrated a high degree of conservation, suggesting that such systems remain functionally similar across chemical environments. The examination of genomic islands unique to our strain revealed the presence of genes involved in carbohydrate metabolism, aromatic carbon metabolism, and carbon turnover, confirmed through phenotypic assays, suggesting the acquisition of potentially novel mechanisms for energy metabolism in this strain. We also identified a twitching motility phenotype active at low-nutrient concentrations that may allow alternative exploratory mechanisms for this organism in a geochemical environment. Two sets of candidate twitching motility genes are present within the genome, one on the chromosome and one on a plasmid; however, a plasmid knockout identified the functional gene as being present on the chromosome. This work highlights the plasticity of the Pseudomonas genome, allowing the acquisition of novel nutrient-scavenging pathways across diverse geochemical environments while maintaining a core of functional stress response genes.
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11
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Analysis of structural MtrC models based on homology with the crystal structure of MtrF. Biochem Soc Trans 2013; 40:1181-5. [PMID: 23176451 DOI: 10.1042/bst20120132] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The outer-membrane decahaem cytochrome MtrC is part of the transmembrane MtrCAB complex required for mineral respiration by Shewanella oneidensis. MtrC has significant sequence similarity to the paralogous decahaem cytochrome MtrF, which has been structurally solved through X-ray crystallography. This now allows for homology-based models of MtrC to be generated. The structure of these MtrC homology models contain ten bis-histidine-co-ordinated c-type haems arranged in a staggered cross through a four-domain structure. This model is consistent with current spectroscopic data and shows that the areas around haem 5 and haem 10, at the termini of an octahaem chain, are likely to have functions similar to those of the corresponding haems in MtrF. The electrostatic surfaces around haem 7, close to the β-barrels, are different in MtrF and MtrC, indicating that these haems may have different potentials and interact with substrates differently.
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12
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Induction of nitrate-dependent Fe(II) oxidation by Fe(II) in Dechloromonas sp. strain UWNR4 and Acidovorax sp. strain 2AN. Appl Environ Microbiol 2012; 79:748-52. [PMID: 23144134 DOI: 10.1128/aem.02709-12] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We evaluated the inducibility of nitrate-dependent Fe(II)-EDTA oxidation (NDFO) in non-growth, chloramphenicol-amended, resting-cell suspensions of Dechloromonas sp. strain UWNR4 and Acidovorax sp. strain 2AN. Cells previously incubated with Fe(II)-EDTA oxidized ca. 6-fold more Fe(II)-EDTA than cells previously incubated with Fe(III)-EDTA. This is the first report of induction of NDFO by Fe(II).
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Ahmad W, Shabbiri K, Adnan A. Exploration of respiratory chain of Nocardia asteroides: purification of succinate quinone oxidoreductase. J Membr Biol 2012; 245:89-95. [PMID: 22359064 DOI: 10.1007/s00232-012-9417-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2011] [Accepted: 01/26/2012] [Indexed: 11/26/2022]
Abstract
Nocardia asteroides is a pathogenic bacterium that causes severe pulmonary infections and plays a vital role in HIV development. Its electron transport chain containing cytochromes as electron carriers is still undiscovered. Information regarding cytochromes is important during drug synthesis based on cytochrome inhibitions. In this study we explored the electron transport of N. asteroides. Spectroscopic analysis of cytoplasm and membranes isolated from N. asteroides indicates the presence of soluble cytochrome-c, complex-II and the modified a(1)c(1) complex as the terminal oxidase. The molecular weight of the respiratory complex-II isolated and purified from the given bacterium was 103 kDa and was composed of three subunits, of 14, 26 and 63 kDa. Complex-II showed symmetrical α-absorption peaks at 561 nm in the reduced state. Spectral analysis revealed the presence of only one heme b molecule (14-kDa subunit) in complex-II, which was confirmed by heme staining. Heme b content was found to be 9.5 nmol/mg in complex-II. The electron transport chain of N. asteroides showed the presence of soluble cytochrome-c, cytochrome-a(1)c(1) and cytochrome-b.
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Affiliation(s)
- Waqar Ahmad
- Department of Chemistry, GC University, Lahore 54000, Pakistan.
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Martinez VD, Vucic EA, Adonis M, Gil L, Lam WL. Arsenic biotransformation as a cancer promoting factor by inducing DNA damage and disruption of repair mechanisms. Mol Biol Int 2011. [PMID: 22091411 DOI: 10.4061/2011/718974]] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Chronic exposure to arsenic in drinking water poses a major global health concern. Populations exposed to high concentrations of arsenic-contaminated drinking water suffer serious health consequences, including alarming cancer incidence and death rates. Arsenic is biotransformed through sequential addition of methyl groups, acquired from s-adenosylmethionine (SAM). Metabolism of arsenic generates a variety of genotoxic and cytotoxic species, damaging DNA directly and indirectly, through the generation of reactive oxidative species and induction of DNA adducts, strand breaks and cross links, and inhibition of the DNA repair process itself. Since SAM is the methyl group donor used by DNA methyltransferases to maintain normal epigenetic patterns in all human cells, arsenic is also postulated to affect maintenance of normal DNA methylation patterns, chromatin structure, and genomic stability. The biological processes underlying the cancer promoting factors of arsenic metabolism, related to DNA damage and repair, will be discussed here.
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Affiliation(s)
- Victor D Martinez
- Department of Integrative Oncology, BC Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC, Canada V5Z 1L3
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Singer E, Emerson D, Webb EA, Barco RA, Kuenen JG, Nelson WC, Chan CS, Comolli LR, Ferriera S, Johnson J, Heidelberg JF, Edwards KJ. Mariprofundus ferrooxydans PV-1 the first genome of a marine Fe(II) oxidizing Zetaproteobacterium. PLoS One 2011; 6:e25386. [PMID: 21966516 PMCID: PMC3179512 DOI: 10.1371/journal.pone.0025386] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2011] [Accepted: 09/02/2011] [Indexed: 12/21/2022] Open
Abstract
Mariprofundus ferrooxydans PV-1 has provided the first genome of the recently discovered Zetaproteobacteria subdivision. Genome analysis reveals a complete TCA cycle, the ability to fix CO(2), carbon-storage proteins and a sugar phosphotransferase system (PTS). The latter could facilitate the transport of carbohydrates across the cell membrane and possibly aid in stalk formation, a matrix composed of exopolymers and/or exopolysaccharides, which is used to store oxidized iron minerals outside the cell. Two-component signal transduction system genes, including histidine kinases, GGDEF domain genes, and response regulators containing CheY-like receivers, are abundant and widely distributed across the genome. Most of these are located in close proximity to genes required for cell division, phosphate uptake and transport, exopolymer and heavy metal secretion, flagellar biosynthesis and pilus assembly suggesting that these functions are highly regulated. Similar to many other motile, microaerophilic bacteria, genes encoding aerotaxis as well as antioxidant functionality (e.g., superoxide dismutases and peroxidases) are predicted to sense and respond to oxygen gradients, as would be required to maintain cellular redox balance in the specialized habitat where M. ferrooxydans resides. Comparative genomics with other Fe(II) oxidizing bacteria residing in freshwater and marine environments revealed similar content, synteny, and amino acid similarity of coding sequences potentially involved in Fe(II) oxidation, signal transduction and response regulation, oxygen sensation and detoxification, and heavy metal resistance. This study has provided novel insights into the molecular nature of Zetaproteobacteria.
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Affiliation(s)
- Esther Singer
- Geomicrobiology Group, Department of Earth Sciences, University of Southern California, Los Angeles, California, United States of America
| | - David Emerson
- Bigelow Laboratory for Ocean Sciences, West Boothbay Harbor, Maine, United States of America
| | - Eric A. Webb
- Department of Biological Sciences, Marine Environmental Biology Section, University of Southern California, Los Angeles, California, United States of America
| | - Roman A. Barco
- Department of Biological Sciences, Marine Environmental Biology Section, University of Southern California, Los Angeles, California, United States of America
| | - J. Gijs Kuenen
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | - William C. Nelson
- Department of Biological Sciences, Marine Environmental Biology Section, University of Southern California, Los Angeles, California, United States of America
| | - Clara S. Chan
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, United States of America
| | - Luis R. Comolli
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Steve Ferriera
- J. Craig Venter Institute, San Diego, California, United States of America
| | - Justin Johnson
- J. Craig Venter Institute, San Diego, California, United States of America
| | - John F. Heidelberg
- Department of Biological Sciences, Marine Environmental Biology Section, University of Southern California, Los Angeles, California, United States of America
| | - Katrina J. Edwards
- Geomicrobiology Group, Department of Earth Sciences, University of Southern California, Los Angeles, California, United States of America
- Department of Biological Sciences, Marine Environmental Biology Section, University of Southern California, Los Angeles, California, United States of America
- * E-mail:
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Martinez VD, Vucic EA, Adonis M, Gil L, Lam WL. Arsenic biotransformation as a cancer promoting factor by inducing DNA damage and disruption of repair mechanisms. Mol Biol Int 2011; 2011:718974. [PMID: 22091411 PMCID: PMC3200225 DOI: 10.4061/2011/718974] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2011] [Accepted: 06/06/2011] [Indexed: 11/20/2022] Open
Abstract
Chronic exposure to arsenic in drinking water poses a major global health concern. Populations exposed to high concentrations of arsenic-contaminated drinking water suffer serious health consequences, including alarming cancer incidence and death rates. Arsenic is biotransformed through sequential addition of methyl groups, acquired from s-adenosylmethionine (SAM). Metabolism of arsenic generates a variety of genotoxic and cytotoxic species, damaging DNA directly and indirectly, through the generation of reactive oxidative species and induction of DNA adducts, strand breaks and cross links, and inhibition of the DNA repair process itself. Since SAM is the methyl group donor used by DNA methyltransferases to maintain normal epigenetic patterns in all human cells, arsenic is also postulated to affect maintenance of normal DNA methylation patterns, chromatin structure, and genomic stability. The biological processes underlying the cancer promoting factors of arsenic metabolism, related to DNA damage and repair, will be discussed here.
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Affiliation(s)
- Victor D Martinez
- Department of Integrative Oncology, BC Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC, Canada V5Z 1L3
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17
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Bird LJ, Bonnefoy V, Newman DK. Bioenergetic challenges of microbial iron metabolisms. Trends Microbiol 2011; 19:330-40. [DOI: 10.1016/j.tim.2011.05.001] [Citation(s) in RCA: 264] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2011] [Revised: 04/30/2011] [Accepted: 05/03/2011] [Indexed: 11/24/2022]
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18
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Hedrich S, Schlömann M, Johnson DB. The iron-oxidizing proteobacteria. Microbiology (Reading) 2011; 157:1551-1564. [DOI: 10.1099/mic.0.045344-0] [Citation(s) in RCA: 400] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The ‘iron bacteria’ are a collection of morphologically and phylogenetically heterogeneous prokaryotes. They include some of the first micro-organisms to be observed and described, and continue to be the subject of a considerable body of fundamental and applied microbiological research. While species of iron-oxidizing bacteria can be found in many different phyla, most are affiliated with the Proteobacteria. The latter can be subdivided into four main physiological groups: (i) acidophilic, aerobic iron oxidizers; (ii) neutrophilic, aerobic iron oxidizers; (iii) neutrophilic, anaerobic (nitrate-dependent) iron oxidizers; and (iv) anaerobic photosynthetic iron oxidizers. Some species (mostly acidophiles) can reduce ferric iron as well as oxidize ferrous iron, depending on prevailing environmental conditions. This review describes what is currently known about the phylogenetic and physiological diversity of the iron-oxidizing proteobacteria, their significance in the environment (on the global and micro scales), and their increasing importance in biotechnology.
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Affiliation(s)
- Sabrina Hedrich
- Interdisciplinary Ecological Center, TU Bergakademie Freiberg, Leipziger Strasse 29, 09599 Freiberg, Germany
- School of Biological Sciences, College of Natural Sciences, Bangor University, Deiniol Road, Bangor LL57 2UW, UK
| | - Michael Schlömann
- Interdisciplinary Ecological Center, TU Bergakademie Freiberg, Leipziger Strasse 29, 09599 Freiberg, Germany
| | - D. Barrie Johnson
- School of Biological Sciences, College of Natural Sciences, Bangor University, Deiniol Road, Bangor LL57 2UW, UK
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19
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Shinada T, Akimoto T, Zhu Y, Goke H, Ohdomari I. Modulation of viability of live cells by focused ion-beam exposure. Biotechnol Bioeng 2011; 108:222-5. [PMID: 20812258 DOI: 10.1002/bit.22917] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Introduction of membrane-impermeant substances into living cells is the key method to understand contemporary cellular processes by investigating cellular responses and phenotypes. Here, we performed gold ion beam exposure into live cells by using the focused ion beam implantation method, which was originally developed to precisely control semiconductor device performances. We evaluated the viability of the gold-irradiated cells by measuring the concentration of adenosine triphosphate (ATP), which is an intracellular energy source produced in the mitochondrial membrane. The viability of the irradiated cells was found to be 20% higher than that of the unirradiated control cells. The atoms might promote the energy generating processes within the mitochondrion. Our results suggest that the viability of living cells can be modulated by accurately controlling the dopant atom numbers. Our technique may be considered as a potential tool in life and medical sciences to quantitatively elucidate the dose-dependent effects of dopants.
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Affiliation(s)
- Takahiro Shinada
- Waseda Institute for Advanced Study, Waseda University, 1-6-1 Nishiwaseda, Shinjuku, Tokyo 169-8050, Japan.
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20
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Bose A, Newman DK. Regulation of the phototrophic iron oxidation (pio) genes in Rhodopseudomonas palustris TIE-1 is mediated by the global regulator, FixK. Mol Microbiol 2010; 79:63-75. [PMID: 21166894 PMCID: PMC3050613 DOI: 10.1111/j.1365-2958.2010.07430.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The pioABC operon is required for phototrophic iron oxidative (photoferrotrophic) growth by the αproteobacterium Rhodopseudomonas palustris TIE-1. Expression analysis of this operon showed that it was transcribed and translated during anaerobic growth, upregulation being observed only under photoferrotrophic conditions. Very low levels of transcription were observed during aerobic growth, suggesting expression was induced by anoxia. The presence of two canonical FixK boxes upstream of the identified pioABC transcription start site implicated FixK as a likely regulator. To test this possibility, a δfixK mutant of R. palustris TIE-1 was assessed for pioABC expression. pioABC expression decreased dramatically in δfixK versus WT during photoferrotrophic growth, implying that FixK positively regulates its expression; coincidently, the onset of iron oxidation was prolonged in this mutant. In contrast, pioABC expression increased in δfixK under all non-photoferrotrophic conditions tested, suggesting the presence of additional levels of regulation. Purified FixK directly bound only the proximal FixK box in gel mobility-shift assays. Mutant expression analysis revealed that FixK regulates anaerobic phototrophic expression of other target genes with FixK binding sites in their promoters. This study shows that FixK regulates key iron metabolism genes in an αproteobacterium, pointing to a departure from the canonical Fur/Irr mode of regulation.
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Affiliation(s)
- Arpita Bose
- Department of Biology, Massachusetts Institute of Technology, Howard Hughes Medical Institute, 77 Massachusetts Ave., 68-380, Cambridge, MA 02139, USA
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21
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Hegler F, Schmidt C, Schwarz H, Kappler A. Does a low-pH microenvironment around phototrophic FeII-oxidizing bacteria prevent cell encrustation by FeIII minerals? FEMS Microbiol Ecol 2010; 74:592-600. [DOI: 10.1111/j.1574-6941.2010.00975.x] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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22
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Label-free bacterial imaging with deep-UV-laser-induced native fluorescence. Appl Environ Microbiol 2010; 76:7231-7. [PMID: 20817797 DOI: 10.1128/aem.00943-10] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We introduce a near-real-time optical imaging method that works via the detection of the intrinsic fluorescence of life forms upon excitation by deep-UV (DUV) illumination. A DUV (<250-nm) source enables the detection of microbes in their native state on natural materials, avoiding background autofluorescence and without the need for fluorescent dyes or tags. We demonstrate that DUV-laser-induced native fluorescence can detect bacteria on opaque surfaces at spatial scales ranging from tens of centimeters to micrometers and from communities to single cells. Given exposure times of 100 μs and low excitation intensities, this technique enables rapid imaging of bacterial communities and cells without irreversible sample alteration or destruction. We also demonstrate the first noninvasive detection of bacteria on in situ-incubated environmental experimental samples from the deep ocean (Lo'ihi Seamount), showing the use of DUV native fluorescence for in situ detection in the deep biosphere and other nutrient-limited environments.
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23
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Salas EC, Berelson WM, Hammond DE, Kampf AR, Nealson KH. The Impact of Bacterial Strain on the Products of Dissimilatory Iron Reduction. GEOCHIMICA ET COSMOCHIMICA ACTA 2010; 74:574-583. [PMID: 20161499 PMCID: PMC2796802 DOI: 10.1016/j.gca.2009.10.039] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Three bacterial strains from the genus Shewanella were used to examine the influence of specific bacteria on the products of dissimilatory iron reduction. Strains CN32, MR-4 and W3-18-1 were incubated with HFO (hydrous ferric oxide) as the terminal electron acceptor and lactate as the organic carbon and energy source. Mineral products of iron reduction were analyzed using X-ray powder diffraction, electron microscopy, coulometry and susceptometry. Under identical nutrient loadings, iron reduction rates for strains CN32 and W3-18-1 were similar, and about twice as fast as MR-4. Qualitative and quantitative assessment of mineralized end products (secondary minerals) indicated that different products were formed during experiments with similar reduction rates but different strains (CN32 and W3-18-1), and similar products were formed during experiments with different iron reduction rates and different strains (CN32 and MR-4). The major product of iron reduction by strains CN32 and MR-4 was magnetite, while for W3-18-1 it was a mixture of magnetite and iron carbonate hydroxide hydrate (green rust), a precursor to fougerite. Another notable difference was that strains CN32 and MR-4 converted all of the starting ferric iron material into magnetite, while W3-18-1 did not convert most of the Fe(3+) into a recognizable crystalline material. Biofilm formation is more robust in W3-18-1 than in the other two strains used in this study. The differences in mineralization may be an indicator that EPS (or another cellular product from W3-18-1) may interfere with the crystallization of magnetite or facilitate formation of green rust. These results suggest that the relative abundance of mineral end products and the relative distribution of these products are strongly dependent on the bacterial species or strain catalyzing iron reduction.
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Affiliation(s)
- Everett C. Salas
- University of Southern California, Department of Earth Sciences
- Corresponding author, present contact:
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24
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Poulain AJ, Newman DK. Rhodobacter capsulatus catalyzes light-dependent Fe(II) oxidation under anaerobic conditions as a potential detoxification mechanism. Appl Environ Microbiol 2009; 75:6639-46. [PMID: 19717624 PMCID: PMC2772431 DOI: 10.1128/aem.00054-09] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2009] [Accepted: 08/22/2009] [Indexed: 11/20/2022] Open
Abstract
Diverse bacteria are known to oxidize millimolar concentrations of ferrous iron [Fe(II)] under anaerobic conditions, both phototrophically and chemotrophically. Yet whether they can do this under conditions that are relevant to natural systems is understood less well. In this study, we tested how light, Fe(II) speciation, pH, and salinity affected the rate of Fe(II) oxidation by Rhodobacter capsulatus SB1003. Although R. capsulatus cannot grow photoautotrophically on Fe(II), it oxidizes Fe(II) at rates comparable to those of bacteria that do grow photoautotrophically on Fe(II) as soon as it is exposed to light, provided it has a functional photosystem. Chelation of Fe(II) by diverse organic ligands promotes Fe(II) oxidation, and as the pH increases, so does the oxidation rate, except in the presence of nitrilotriacetate; nonchelated forms of Fe(II) are also more rapidly oxidized at higher pH. Salt concentrations typical of marine environments inhibit Fe(II) oxidation. When growing photoheterotrophically on humic substances, R. capsulatus is highly sensitive to low concentrations of Fe(II); it is inhibited in the presence of concentrations as low as 5 microM. The product of Fe(II) oxidation, ferric iron, does not hamper growth under these conditions. When other parameters, such as pH or the presence of chelators, are adjusted to promote Fe(II) oxidation, the growth inhibition effect of Fe(II) is alleviated. Together, these results suggest that Fe(II) is toxic to R. capsulatus growing under strictly anaerobic conditions and that Fe(II) oxidation alleviates this toxicity.
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Affiliation(s)
- Alexandre J. Poulain
- Biaology Department, Massachusetts Institute of Technology, 68-380, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, Earth, Atmospheric and Planetary Sciences Department, Massachusetts Institute of Technology, 68-380, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, Howard Hughes Medical Institute, 68-380, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139
| | - Dianne K. Newman
- Biaology Department, Massachusetts Institute of Technology, 68-380, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, Earth, Atmospheric and Planetary Sciences Department, Massachusetts Institute of Technology, 68-380, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, Howard Hughes Medical Institute, 68-380, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139
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25
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Uroz S, Calvaruso C, Turpault MP, Frey-Klett P. Mineral weathering by bacteria: ecology, actors and mechanisms. Trends Microbiol 2009; 17:378-87. [PMID: 19660952 DOI: 10.1016/j.tim.2009.05.004] [Citation(s) in RCA: 193] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2008] [Revised: 05/15/2009] [Accepted: 05/26/2009] [Indexed: 12/31/2022]
Affiliation(s)
- Stéphane Uroz
- Institut National de la Recherche Agronomique (INRA), Nancy Université, UMR 1136 Interactions Arbres Micro-organismes, Centre INRA de Nancy, 54280 Champenoux, France.
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26
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Wang W, Shao Z, Liu Y, Wang G. Removal of multi-heavy metals using biogenic manganese oxides generated by a deep-sea sedimentary bacterium – Brachybacterium sp. strain Mn32. Microbiology (Reading) 2009; 155:1989-1996. [DOI: 10.1099/mic.0.024141-0] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A deep-sea manganese-oxidizing bacterium,Brachybacteriumsp. strain Mn32, showed high Mn(II) resistance (MIC 55 mM) and Mn(II)-oxidizing/removing abilities. Strain Mn32 removed Mn(II) by two pathways: (1) oxidizing soluble Mn(II) to insoluble biogenic Mn oxides – birnessite (δ-MnO2group) and manganite (γ-MnOOH); (2) the biogenic Mn oxides further adsorb more Mn(II) from the culture. The generated biogenic Mn oxides surround the cell surfaces of strain Mn32 and provide a high capacity to adsorb Zn(II) and Ni(II). Mn(II) oxidation by strain Mn32 was inhibited by both sodium azide ando-phenanthroline, suggesting the involvement of a metalloenzyme which was induced by Mn(II). X-ray diffraction analysis showed that the crystal structures of the biogenic Mn oxides were different from those of commercial pyrolusite (β-MnO2group) and fresh chemically synthesized vernadite (δ-MnO2group). The biogenic Mn oxides generated by strain Mn32 showed two to three times higher Zn(II) and Ni(II) adsorption abilities than commercial and fresh synthetic MnO2. The crystal structure and the biogenic MnO2types may be important factors for the high heavy metal adsorption ability of strain Mn32. This study provides potential applications of a new marine Mn(II)-oxidizing bacterium in heavy metal bioremediation and increases our basic knowledge of microbial manganese oxidation mechanisms.
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Affiliation(s)
- Wenming Wang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Zongze Shao
- The Third Institute of Oceanography, State Oceanic Administration, Xiamen 361005, PR China
| | - Yanjun Liu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Gejiao Wang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
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27
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The tetraheme cytochrome from Shewanella oneidensis MR-1 shows thermodynamic bias for functional specificity of the hemes. J Biol Inorg Chem 2008; 14:375-85. [DOI: 10.1007/s00775-008-0455-7] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2008] [Accepted: 11/14/2008] [Indexed: 10/21/2022]
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28
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Mechanism and Consequences of anaerobic respiration of cobalt by Shewanella oneidensis strain MR-1. Appl Environ Microbiol 2008; 74:6880-6. [PMID: 18836009 DOI: 10.1128/aem.00840-08] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacteria from the genus Shewanella are the most diverse respiratory organisms studied to date and can utilize a variety of metals and metal(loid)s as terminal electron acceptors. These bacteria can potentially be used in bioremediation applications since the redox state of metals often influences both solubility and toxicity. Understanding molecular mechanisms by which metal transformations occur and the consequences of by-products that may be toxic to the organism and thus inhibitory to the overall process is significant to future applications for bioremediation. Here, we examine the ability of Shewanella oneidensis to catalyze the reduction of chelated cobalt. We describe an unexpected ramification of [Co(III)-EDTA](-) reduction by S. oneidensis: the formation of a toxic by-product. We found that [Co(II)-EDTA](2-), the product of [Co(III)-EDTA](-) respiration, inhibited the growth of S. oneidensis strain MR-1 and that this toxicity was partially abolished by the addition of MgSO(4). We demonstrate that [Co(III)-EDTA](-) reduction by S. oneidensis requires the Mtr extracellular respiratory pathway and associated pathways required to develop functional Mtr enzymes (the c-type cytochrome maturation pathway) and ensure proper localization (type II secretion). The Mtr pathway is known to be required for a variety of substrates, including some chelated and insoluble metals and organic compounds. Understanding the full substrate range for the Mtr pathway is crucial for developing S. oneidensis strains as a tool for bioremediation.
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29
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Castelle C, Guiral M, Malarte G, Ledgham F, Leroy G, Brugna M, Giudici-Orticoni MT. A new iron-oxidizing/O2-reducing supercomplex spanning both inner and outer membranes, isolated from the extreme acidophile Acidithiobacillus ferrooxidans. J Biol Chem 2008; 283:25803-11. [PMID: 18632666 PMCID: PMC3258861 DOI: 10.1074/jbc.m802496200] [Citation(s) in RCA: 132] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2008] [Revised: 07/16/2008] [Indexed: 01/23/2023] Open
Abstract
The iron respiratory chain of the acidophilic bacterium Acidithiobacillus ferrooxidans involves various metalloenzymes. Here we demonstrate that the oxygen reduction pathway from ferrous iron (named downhill pathway) is organized as a supercomplex constituted of proteins located in the outer and inner membranes as well as in the periplasm. For the first time, the outer membrane-bound cytochrome c Cyc2 was purified, and we showed that it is responsible for iron oxidation and determined that its redox potential is the highest measured to date for a cytochrome c. The organization of metalloproteins inside the supramolecular structure was specified by protein-protein interaction experiments. The isolated complex spanning the two membranes had iron oxidase as well as oxygen reductase activities, indicating functional electron transfer between the first iron electron acceptor, Cyc2, and the Cu(A) center of cytochrome c oxidase aa(3). This is the first characterization of a respirasome from an acidophilic bacterium. In Acidithiobacillus ferrooxidans,O(2) reduction from ferrous iron must be coupled to the energy-consuming reduction of NAD(+)(P) from ferrous iron (uphill pathway) required for CO(2) fixation and other anabolic processes. Besides the proteins involved in the O(2) reduction, there were additional proteins in the supercomplex, involved in uphill pathway (bc complex and cytochrome Cyc(42)), suggesting a possible physical link between these two pathways.
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Abstract
The shewanellae are aquatic microorganisms with worldwide distribution. Their hallmark features include unparalleled respiratory diversity and the capacity to thrive at low temperatures. As a genus the shewanellae are physiologically diverse, and this review provides an overview of the varied roles they serve in the environment and describes what is known about how they might survive in such extreme and harsh environments. In light of their fascinating physiology, these organisms have several biotechnological uses, from bioremediation of chlorinated compounds, radionuclides, and other environmental pollutants to energy-generating biocatalysis. The ecology and biotechnology of these organisms are intertwined, with genomics playing a key role in our understanding of their physiology.
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Affiliation(s)
- Heidi H Hau
- Department of Microbiology and The BioTechnology Institute, University of Minnesota, St. Paul, Minnesota 55108, USA
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32
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Abstract
Although it has long been known that microbes can generate energy using diverse strategies, only recently has it become clear that a growing number involve electron transfer to or from extracellular substrates. The best-known example of what we will term 'extracellular respiration' is electron transfer between microbes and minerals, such as iron and manganese (hydr)oxides. This makes sense, given that these minerals are sparingly soluble. What is perhaps surprising, however, is that a number of substrates that might typically be classified as 'soluble' are also respired at the cell surface. There are several reasons why this might be the case: the substrate, in its ecological context, might be associated with a solid surface and thus effectively insoluble; the substrate, while soluble, might simply be too large to transport inside the cell; or the substrate, while benign in one redox state, might become toxic after it is metabolized. In this review, we discuss various examples of extracellular respiration, paying particular attention to what is known about the molecular mechanisms underlying these processes. As will become clear, much remains to be learned about the biochemistry, cell biology and regulation of extracellular respiration, making it a rich field of study for molecular microbiologists.
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Affiliation(s)
- Jeffrey A Gralnick
- Department of Microbiology, University of Minnesota, Saint Paul, MN, USA.
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Heimann AC, Blodau C, Postma D, Larsen F, Viet PH, Nhan PQ, Jessen S, Duc MT, Hue NTM, Jakobsen R. Hydrogen thresholds and steady-state concentrations associated with microbial arsenate respiration. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2007; 41:2311-7. [PMID: 17438780 DOI: 10.1021/es062067d] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
H2 thresholds for microbial respiration of arsenate (As(V)) were investigated in a pure culture of Sulfurospirillum arsenophilum. H2 was consumed to threshold concentrations of 0.03-0.09 nmol/L with As(V) as terminal electron acceptor, allowing for a Gibbs free-energy yield of 36-41 kJ per mol of reaction. These thresholds are among the lowest measured for anaerobic respirers and fall into the range of denitrifiers or Fe(III)-reducers. In sediments from an arsenic-contaminated aquifer in the Red River flood plain, Vietnam, H2 levels decreased to 0.4-2 nmol/L when As(V) was added under anoxic conditions. When As-(V) was depleted, H2 concentrations rebounded by a factor of 10, a level similar to that observed in arsenic-free controls. The sediment-associated microbial population completely reduced millimolar levels of As(V) to arsenite (As-(III)) within a few days. The rate of As(V)-reduction was essentially the same in sediments amended with a pure culture of S. arsenophilum. These findings together with a review of observed H2 threshold and steady-state values suggest that microbial As(V)-respirers have a competitive advantage over several other anaerobic respirers through their ability to thrive at low H2 levels.
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Affiliation(s)
- Axel C Heimann
- Institute of Environment & Resources, Bygningstorvet, Building 115, Technical University of Denmark, DK-2800 Lyngby, Denmark.
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Bouskill NJ, Barnhart EP, Galloway TS, Handy RD, Ford TE. Quantification of changing Pseudomonas aeruginosa sodA, htpX and mt gene abundance in response to trace metal toxicity: a potential in situ biomarker of environmental health. FEMS Microbiol Ecol 2007; 60:276-86. [PMID: 17374126 DOI: 10.1111/j.1574-6941.2007.00296.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Sediment-dwelling prokaryotes play a vital role in determining the fate and speciation of metals, yet are also susceptible to the biological effects of trace metals. In this article, optimized DNA extraction and purification techniques and species-specific primers are used to assess the genetic incidence and abundance of metal detoxification and general stress genes of Pseudomonas aeruginosa to complement chemical analysis in inferring the severity of metal-contaminated sites along the Clark Fork River, Montana. Results show the highest incidence of candidate genes related to bacterial stress at the most polluted site, while multiple regression analysis demonstrated significant correlations (P<0.05, r(2)=0.9) between in situ metal concentrations (As, Cu and Zn), total gene incidence, and the incidence of metal detoxification genes. Furthermore, principal components plotting the incidence of genes related to metal resistance show clear separation of sites giving clear clusters on the basis of contamination. Quantification of three genes (sodA, htpX and mt) from surveyed sites found significantly higher (anova, P<0.05) copy numbers at the more contaminated sites compared with reference sites. The development of rapid microbial biomarker tools represents a significant advance in the field of environmental biomonitoring and the prediction of metal bioavailability.
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Affiliation(s)
- Nicolas J Bouskill
- Department of Microbiology, Montana State University, Bozeman, MT 59717, USA.
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35
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Jiao Y, Newman DK. The pio operon is essential for phototrophic Fe(II) oxidation in Rhodopseudomonas palustris TIE-1. J Bacteriol 2007; 189:1765-73. [PMID: 17189359 PMCID: PMC1855732 DOI: 10.1128/jb.00776-06] [Citation(s) in RCA: 174] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2006] [Accepted: 12/12/2006] [Indexed: 11/20/2022] Open
Abstract
Phototrophic Fe(II)-oxidizing bacteria couple the oxidation of ferrous iron [Fe(II)] to reductive CO(2) fixation by using light energy, but until recently, little has been understood about the molecular basis for this process. Here we report the discovery, with Rhodopseudomonas palustris TIE-1 as a model organism, of a three-gene operon, designated the pio operon (for phototrophic iron oxidation), that is necessary for phototrophic Fe(II) oxidation. The first gene in the operon, pioA, encodes a c-type cytochrome that is upregulated under Fe(II)-grown conditions. PioA contains a signal sequence and shares homology with MtrA, a decaheme c-type cytochrome from Shewanella oneidensis MR-1. The second gene, pioB, encodes a putative outer membrane beta-barrel protein. PioB is a homologue of MtrB from S. oneidensis MR-1. The third gene, pioC, encodes a putative high potential iron sulfur protein (HiPIP) with a twin-arginine translocation (Tat) signal sequence and is similar to the putative Fe(II) oxidoreductase (Iro) from Acidithiobacillus ferrooxidans. Like PioA, PioB and PioC appear to be secreted proteins. Deletion of the pio operon results in loss of Fe(II) oxidation activity and growth on Fe(II). Complementation studies confirm that the phenotype of this mutant is due to loss of the pio genes. Deletion of pioA alone results in loss of almost all Fe(II) oxidation activity; however, deletion of either pioB or pioC alone results in only partial loss of Fe(II) oxidation activity. Together, these results suggest that proteins encoded by the pio operon are essential and specific for phototrophic Fe(II) oxidation in R. palustris TIE-1.
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Affiliation(s)
- Yongqin Jiao
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA 91125, USA
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Croal LR, Jiao Y, Newman DK. The fox operon from Rhodobacter strain SW2 promotes phototrophic Fe(II) oxidation in Rhodobacter capsulatus SB1003. J Bacteriol 2006; 189:1774-82. [PMID: 17189371 PMCID: PMC1855712 DOI: 10.1128/jb.01395-06] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Anoxygenic photosynthesis based on Fe(II) is thought to be one of the most ancient forms of metabolism and is hypothesized to represent a transition step in the evolution of oxygenic photosynthesis. However, little is known about the molecular basis of this process because, until recently (Y. Jiao and D. K. Newman, J. Bacteriol. 189:1765-1773, 2007), most phototrophic Fe(II)-oxidizing bacteria have been genetically intractable. In this study, we circumvented this problem by taking a heterologous-complementation approach to identify a three-gene operon (the foxEYZ operon) from Rhodobacter sp. strain SW2 that confers enhanced light-dependent Fe(II) oxidation activity when expressed in its genetically tractable relative Rhodobacter capsulatus SB1003. The first gene in this operon, foxE, encodes a c-type cytochrome with no significant similarity to other known proteins. Expression of foxE alone confers significant light-dependent Fe(II) oxidation activity on SB1003, but maximal activity is achieved when foxE is expressed with the two downstream genes foxY and foxZ. In SW2, the foxE and foxY genes are cotranscribed in the presence of Fe(II) and/or hydrogen, with foxZ being transcribed only in the presence of Fe(II). Sequence analysis predicts that foxY encodes a protein containing the redox cofactor pyrroloquinoline quinone and that foxZ encodes a protein with a transport function. Future biochemical studies will permit the localization and function of the Fox proteins in SW2 to be determined.
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Affiliation(s)
- Laura R Croal
- California Institute of Technology, Pasadena, CA 91125, USA
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Meshulam-Simon G, Behrens S, Choo AD, Spormann AM. Hydrogen metabolism in Shewanella oneidensis MR-1. Appl Environ Microbiol 2006; 73:1153-65. [PMID: 17189435 PMCID: PMC1828657 DOI: 10.1128/aem.01588-06] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Shewanella oneidensis MR-1 is a facultative sediment microorganism which uses diverse compounds, such as oxygen and fumarate, as well as insoluble Fe(III) and Mn(IV) as electron acceptors. The electron donor spectrum is more limited and includes metabolic end products of primary fermenting bacteria, such as lactate, formate, and hydrogen. While the utilization of hydrogen as an electron donor has been described previously, we report here the formation of hydrogen from pyruvate under anaerobic, stationary-phase conditions in the absence of an external electron acceptor. Genes for the two S. oneidensis MR-1 hydrogenases, hydA, encoding a periplasmic [Fe-Fe] hydrogenase, and hyaB, encoding a periplasmic [Ni-Fe] hydrogenase, were found to be expressed only under anaerobic conditions during early exponential growth and into stationary-phase growth. Analyses of DeltahydA, DeltahyaB, and DeltahydA DeltahyaB in-frame-deletion mutants indicated that HydA functions primarily as a hydrogen-forming hydrogenase while HyaB has a bifunctional role and represents the dominant hydrogenase activity under the experimental conditions tested. Based on results from physiological and genetic experiments, we propose that hydrogen is formed from pyruvate by multiple parallel pathways, one pathway involving formate as an intermediate, pyruvate-formate lyase, and formate-hydrogen lyase, comprised of HydA hydrogenase and formate dehydrogenase, and a formate-independent pathway involving pyruvate dehydrogenase. A reverse electron transport chain is potentially involved in a formate-hydrogen lyase-independent pathway. While pyruvate does not support a fermentative mode of growth in this microorganism, pyruvate, in the absence of an electron acceptor, increased cell viability in anaerobic, stationary-phase cultures, suggesting a role in the survival of S. oneidensis MR-1 under stationary-phase conditions.
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Affiliation(s)
- Galit Meshulam-Simon
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA 94305-5429, USA
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Cruz-García C, Murray AE, Klappenbach JA, Stewart V, Tiedje JM. Respiratory nitrate ammonification by Shewanella oneidensis MR-1. J Bacteriol 2006; 189:656-62. [PMID: 17098906 PMCID: PMC1797406 DOI: 10.1128/jb.01194-06] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Anaerobic cultures of Shewanella oneidensis MR-1 grown with nitrate as the sole electron acceptor exhibited sequential reduction of nitrate to nitrite and then to ammonium. Little dinitrogen and nitrous oxide were detected, and no growth occurred on nitrous oxide. A mutant with the napA gene encoding periplasmic nitrate reductase deleted could not respire or assimilate nitrate and did not express nitrate reductase activity, confirming that the NapA enzyme is the sole nitrate reductase. Hence, S. oneidensis MR-1 conducts respiratory nitrate ammonification, also termed dissimilatory nitrate reduction to ammonium, but not respiratory denitrification.
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Affiliation(s)
- Claribel Cruz-García
- Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824-1325, USA
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Abstract
Arsenic and selenium are readily metabolized by prokaryotes, participating in a full range of metabolic functions including assimilation, methylation, detoxification, and anaerobic respiration. Arsenic speciation and mobility is affected by microbes through oxidation/reduction reactions as part of resistance and respiratory processes. A robust arsenic cycle has been demonstrated in diverse environments. Respiratory arsenate reductases, arsenic methyltransferases, and new components in arsenic resistance have been recently described. The requirement for selenium stems primarily from its incorporation into selenocysteine and its function in selenoenzymes. Selenium oxyanions can serve as an electron acceptor in anaerobic respiration, forming distinct nanoparticles of elemental selenium that may be enriched in (76)Se. The biogenesis of selenoproteins has been elucidated, and selenium methyltransferases and a respiratory selenate reductase have also been described. This review highlights recent advances in ecology, biochemistry, and molecular biology and provides a prelude to the impact of genomics studies.
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Affiliation(s)
- John F Stolz
- Department of Biological Sciences, Duquesne University, Pittsburgh, Pennsylvania 15282, USA.
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Gralnick JA, Vali H, Lies DP, Newman DK. Extracellular respiration of dimethyl sulfoxide by Shewanella oneidensis strain MR-1. Proc Natl Acad Sci U S A 2006; 103:4669-74. [PMID: 16537430 PMCID: PMC1450229 DOI: 10.1073/pnas.0505959103] [Citation(s) in RCA: 168] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Shewanella species are renowned for their respiratory versatility, including their ability to respire poorly soluble substrates by using enzymatic machinery that is localized to the outside of the cell. The ability to engage in "extracellular respiration" to date has focused primarily on respiration of minerals. Here, we identify two gene clusters in Shewanella oneidensis strain MR-1 that each contain homologs of genes required for metal reduction and genes that are predicted to encode dimethyl sulfoxide (DMSO) reductase subunits. Molecular and genetic analyses of these clusters indicate that one (SO1427-SO1432) is required for anaerobic respiration of DMSO. We show that DMSO respiration is an extracellular respiratory process through the analysis of mutants defective in type II secretion, which is required for transporting proteins to the outer membrane in Shewanella. Moreover, immunogold labeling of DMSO reductase subunits reveals that they reside on the outer leaflet of the outer membrane under anaerobic conditions. The extracellular localization of the DMSO reductase in S. oneidensis suggests these organisms may perceive DMSO in the environment as an insoluble compound.
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Affiliation(s)
- Jeffrey A Gralnick
- Divisions of Geological and Planetary Sciences and Biology, and Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA 91125, USA.
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Haratake M, Yasumoto K, Ono M, Akashi M, Nakayama M. Synthesis of hydrophilic macroporous chelating polymers and their versatility in the preconcentration of metals in seawater samples. Anal Chim Acta 2006. [DOI: 10.1016/j.aca.2006.01.042] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Lies DP, Hernandez ME, Kappler A, Mielke RE, Gralnick JA, Newman DK. Shewanella oneidensis MR-1 uses overlapping pathways for iron reduction at a distance and by direct contact under conditions relevant for Biofilms. Appl Environ Microbiol 2005; 71:4414-26. [PMID: 16085832 PMCID: PMC1183279 DOI: 10.1128/aem.71.8.4414-4426.2005] [Citation(s) in RCA: 253] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We developed a new method to measure iron reduction at a distance based on depositing Fe(III) (hydr)oxide within nanoporous glass beads. In this "Fe-bead" system, Shewanella oneidensis reduces at least 86.5% of the iron in the absence of direct contact. Biofilm formation accompanies Fe-bead reduction and is observable both macro- and microscopically. Fe-bead reduction is catalyzed by live cells adapted to anaerobic conditions, and maximal reduction rates require sustained protein synthesis. The amount of reactive ferric iron in the Fe-bead system is available in excess such that the rate of Fe-bead reduction is directly proportional to cell density; i.e., it is diffusion limited. Addition of either lysates prepared from anaerobic cells or exogenous electron shuttles stimulates Fe-bead reduction by S. oneidensis, but iron chelators or additional Fe(II) do not. Neither dissolved Fe(III) nor electron shuttling activity was detected in culture supernatants, implying that the mediator is retained within the biofilm matrix. Strains with mutations in omcB or mtrB show about 50% of the wild-type levels of reduction, while a cymA mutant shows less than 20% of the wild-type levels of reduction and a menF mutant shows insignificant reduction. The Fe-bead reduction defect of the menF mutant can be restored by addition of menaquinone, but menaquinone itself cannot stimulate Fe-bead reduction. Because the menF gene encodes the first committed step of menaquinone biosynthesis, no intermediates of the menaquinone biosynthetic pathway are used as diffusible mediators by this organism to promote iron reduction at a distance. CymA and menaquinone are required for both direct and indirect mineral reduction, whereas MtrB and OmcB contribute to but are not absolutely required for iron reduction at a distance.
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Affiliation(s)
- Douglas P Lies
- Department of Geological and Planetary Sciences, Caltech, Pasadena, CA 91125, USA
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Jiao Y, Kappler A, Croal LR, Newman DK. Isolation and characterization of a genetically tractable photoautotrophic Fe(II)-oxidizing bacterium, Rhodopseudomonas palustris strain TIE-1. Appl Environ Microbiol 2005; 71:4487-96. [PMID: 16085840 PMCID: PMC1183355 DOI: 10.1128/aem.71.8.4487-4496.2005] [Citation(s) in RCA: 115] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2004] [Accepted: 03/11/2005] [Indexed: 11/20/2022] Open
Abstract
We report the isolation and characterization of a phototrophic ferrous iron [Fe(II)]-oxidizing bacterium named TIE-1 that differs from other Fe(II)-oxidizing phototrophs in that it is genetically tractable. Under anaerobic conditions, TIE-1 grows photoautotrophically with Fe(II), H2, or thiosulfate as the electron donor and photoheterotrophically with a variety of organic carbon sources. TIE-1 also grows chemoheterotrophically in the dark. This isolate appears to be a new strain of the purple nonsulfur bacterial species Rhodopseudomonas palustris, based on physiological and phylogenetic analysis. Fe(II) oxidation is optimal at pH 6.5 to 6.9. The mineral products of Fe(II) oxidation are pH dependent: below pH 7.0 goethite (alpha-FeOOH) forms, and above pH 7.2 magnetite (Fe3O4) forms. TIE-1 forms colonies on agar plates and is sensitive to a variety of antibiotics. A hyperactive mariner transposon is capable of random insertion into the chromosome with a transposition frequency of approximately 10(-5). To identify components involved in phototrophic Fe(II) oxidation, mutants of TIE-1 were generated by transposon mutagenesis and screened for defects in Fe(II) oxidation in a cell suspension assay. Among approximately 12,000 mutants screened, 6 were identified that are specifically impaired in Fe(II) oxidation. Five of these mutants have independent disruptions in a gene that is predicted to encode an integral membrane protein that appears to be part of an ABC transport system; the sixth mutant has an insertion in a gene that is a homolog of CobS, an enzyme involved in cobalamin (vitamin B12) biosynthesis.
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Affiliation(s)
- Yongqin Jiao
- California Institute of Technology, Division of Geological and Planetary Sciences, Mail Stop 100-23, Pasadena, CA 91125, USA
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Oremland RS, Capone DG, Stolz JF, Fuhrman J. Whither or wither geomicrobiology in the era of 'community metagenomics'. Nat Rev Microbiol 2005; 3:572-8. [PMID: 15953928 DOI: 10.1038/nrmicro1182] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Molecular techniques are valuable tools that can improve our understanding of the structure of microbial communities. They provide the ability to probe for life in all niches of the biosphere, perhaps even supplanting the need to cultivate microorganisms or to conduct ecophysiological investigations. However, an overemphasis and strict dependence on such large information-driven endeavours as environmental metagenomics could overwhelm the field, to the detriment of microbial ecology. We now call for more balanced, hypothesis-driven research efforts that couple metagenomics with classic approaches.
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Affiliation(s)
- Ronald S Oremland
- US Geological Survey, 345 Middlefield Road, m/s 480, Menlo Park, California 94025, USA.
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Abstract
The health of tens of millions of people world-wide is at risk from drinking arsenic-contaminated well water. In most cases this arsenic occurs naturally within the sub-surface aquifers, rather than being derived from identifiable point sources of pollution. The mobilization of arsenic into the aqueous phase is the first crucial step in a process that eventually leads to human arsenicosis. Increasing evidence suggests that this is a microbiological phenomenon.
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