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Namgung S, Kwon MJ, Qafoku NP, Lee G. Cr(OH)3(s) oxidation induced by surface catalyzed Mn(II) oxidation. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2014; 48:10760-10768. [PMID: 25144300 DOI: 10.1021/es503018u] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
We examined the feasibility of Cr(OH)3(s) oxidation mediated by surface catalyzed Mn(II) oxidation under common groundwater pH conditions as a potential pathway of natural Cr(VI) contaminations. Dissolved Mn(II) (50 μM) was reacted with or without synthesized Cr(OH)3(s) (1.0 g/L) at pH 7.0-9.0 under oxic or anoxic conditions. Homogeneous Mn(II) oxidation by dissolved O2 was not observed at pH ≤ 8.0 for 50 days. At pH 9.0, by contrast, dissolved Mn(II) was completely removed within 8 days and precipitated as hausmannite. When Cr(OH)3(s) was present, this solid was oxidized and released substantial amounts of Cr(VI) as dissolved Mn(II) was added into the suspension at pH ≥ 8.0 under oxic conditions. Production of Cr(VI) was attributed to Cr(OH)3(s) oxidation by a newly formed Mn oxide via Mn(II) oxidation catalyzed on Cr(OH)3(s) surface. XANES results indicated that this surface-catalyzed Mn(II) oxidation produced a mixed valence Mn(III/IV) solid phase. Our results suggest that toxic Cr(VI) can be naturally produced via Cr(OH)3(s) oxidation coupled with the oxidation of dissolved Mn(II). In addition, this study evokes the potential environmental hazard of sparingly soluble Cr(OH)3(s), which has been considered the most common and a stable remediation product of Cr(VI) contamination.
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Affiliation(s)
- Seonyi Namgung
- Department of Earth System Sciences, Yonsei University , 50 Yonsei-ro, Seodaemun-gu, Seoul 120-749, Republic of Korea
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Heterologous expression and characterization of the manganese-oxidizing protein from Erythrobacter sp. strain SD21. Appl Environ Microbiol 2014; 80:6837-42. [PMID: 25172859 DOI: 10.1128/aem.01873-14] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The manganese (Mn)-oxidizing protein (MopA) from Erythrobacter sp. strain SD21 is part of a unique enzymatic family that is capable of oxidizing soluble Mn(II). This enzyme contains two domains, an animal heme peroxidase domain, which contains the catalytic site, followed by a C-terminal calcium binding domain. Different from the bacterial Mn-oxidizing multicopper oxidase enzymes, little is known about MopA. To gain a better understanding of MopA and its role in Mn(II) oxidation, the 238-kDa full-length protein and a 105-kDa truncated protein containing only the animal heme peroxidase domain were cloned and heterologously expressed in Escherichia coli. Despite having sequence similarity to a peroxidase, hydrogen peroxide did not stimulate activity, nor was activity significantly decreased in the presence of catalase. Both pyrroloquinoline quinone (PQQ) and hemin increased Mn-oxidizing activity, and calcium was required. The Km for Mn(II) of the full-length protein in cell extract was similar to that of the natively expressed protein, but the Km value for the truncated protein in cell extract was approximately 6-fold higher than that of the full-length protein, suggesting that the calcium binding domain may aid in binding Mn(II). Characterization of the heterologously expressed MopA has provided additional insight into the mechanism of bacterial Mn(II) oxidation, which will aid in understanding the role of MopA and Mn oxidation in bioremediation and biogeochemical cycling.
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Ettoumi B, Guesmi A, Brusetti L, Borin S, Najjari A, Boudabous A, Cherif A. Microdiversity of deep-sea Bacillales isolated from Tyrrhenian sea sediments as revealed by ARISA, 16S rRNA gene sequencing and BOX-PCR fingerprinting. Microbes Environ 2013; 28:361-9. [PMID: 24005887 PMCID: PMC4070960 DOI: 10.1264/jsme2.me13013] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
With respect to their terrestrial relatives, marine Bacillales have not been sufficiently investigated. In this report, the diversity of deep-sea Bacillales, isolated from seamount and non-seamount stations at 3,425 to 3,580 m depth in the Tyrrhenian Sea, was investigated using PCR fingerprinting and 16S rRNA sequence analysis. The isolate collection (n=120) was de-replicated by automated ribosomal intergenic spacer analysis (ARISA), and phylogenetic diversity was analyzed by 16S rRNA gene sequencing of representatives of each ARISA haplotype (n=37). Phylogenetic analysis of isolates showed their affiliation to six different genera of low G+C% content Gram-positive Bacillales: Bacillus, Staphylococcus, Exiguobacterium, Paenibacillus, Lysinibacillus and Terribacillus. Bacillus was the dominant genus represented by the species B. licheniformis, B. pumilus, B. subtilis, B. amyloliquefaciens and B. firmus, typically isolated from marine sediments. The most abundant species in the collection was B. licheniformis (n=85), which showed seven distinct ARISA haplotypes with haplotype H8 being the most dominant since it was identified by 63 isolates. The application of BOX-PCR fingerprinting to the B. licheniformis sub-collection allowed their separation into five distinct BOX genotypes, suggesting a high level of intraspecies diversity among marine B. licheniformis strains. This species also exhibited distinct strain distribution between seamount and non-seamount stations and was shown to be highly prevalent in non-seamount stations. This study revealed the great microdiversity of marine Bacillales and contributes to understanding the biogeographic distribution of marine bacteria in deep-sea sediments.
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Affiliation(s)
- Besma Ettoumi
- LR Microorganisms and Active Biomolecules, Faculty of Sciences of Tunis, University of Tunis El Manar
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Microbial Community Analysis in Bio-Filter Bed of Iron and Manganese Removal Treating High Iron, Manganese and Ammonia Nitrogen Groundwater. ACTA ACUST UNITED AC 2013. [DOI: 10.4028/www.scientific.net/amr.777.238] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The integrated process of spray aeration, falling water aeration and bio-filter bed was used for treating groundwater with high iron, manganese and ammonia nitrogen (NH4+-N). The removal efficiencies of iron, manganese and NH4+-N reached 99.1%, 95.0% and 85.2%, and corresponding effluent iron and manganese decreased to 0.1 and 0.05 mg/L. Microbial analysis results indicated that theβ-Proteobacteriawas predominant microorganisms, in whichGallionellaandLeptothrixwere main iron-removal bacteria and manganese-removal bacteria, respectively. Simultaneously,Pseudomona, belonged toγ-Proteobacteria, could absorb and oxidize free manganese to be manganese dioxide (MnO2) by extracellular oxidase.
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Chang J, Tani Y, Naitou H, Miyata N, Seyama H. Fungal mn oxides supporting Mn(II) oxidase activity as effective Mn(II) sequestering materials. ENVIRONMENTAL TECHNOLOGY 2013; 34:2781-2787. [PMID: 24527642 DOI: 10.1080/09593330.2013.790066] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
We examined the Mn(II)-oxidizing ability of the biogenic Mn oxide (BMO) formed in cultures ofa Mn(II)-oxidizing fungus, Acremonium strictum strain KR21-2. The newly formed BMO effectively sequestered dissolved Mn(II) mainly by oxidizing Mn(II) to insoluble Mn under air-equilibrated conditions, and this ability lasted for at least 8 days. Deaerating the BMOs, poisoning them with NaN3, or heating them all readily weakened their Mn(II) oxidation ability, indicating the involvement of enzymatic Mn(II) oxidation. There was no Mn(II)-oxidizing ability observed for mycelia cultivated without Mn(II) or for residual mycelia after the BMO phase was dissolved, suggesting the need for the oxide phase. A sodium dodecyl sulphate-polyacrylamide gel electrophoresis assay demonstrated that the oxide phase embeds the Mn(II) oxidase and thereby maintains the enzymatic activity in BMOs. Freezing at -80 degrees C preserved the Mn(II)-oxidizing ability in BMOs for at least 4 weeks, while lyophilization caused a complete loss of this ability. Based on these results, we propose that fungal Mn oxides supporting Mn(II) oxidase activity are an effective Mn(II)-sequestering material capable of oxidizing Mn(II) continuously from solutions containing no additional nutrients to maintain biological activity.
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Affiliation(s)
- Jianing Chang
- Department of Environmental Health Sciences, Graduate School of Nutritional and Environmental Sciences, University of Shizuoka, Shizuoka, Japan
| | - Yukinori Tani
- Department of Environmental Health Sciences, Graduate School of Nutritional and Environmental Sciences, University of Shizuoka, Shizuoka, Japan
| | - Hirotaka Naitou
- Department of Environmental Health Sciences, Graduate School of Nutritional and Environmental Sciences, University of Shizuoka, Shizuoka, Japan
| | - Naoyuki Miyata
- Department of Biological Environment, Akita Prefectural University, Akita, Japan
| | - Haruhiko Seyama
- National Institute for Environmental Studies, Tsukuba, Japan
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Butterfield CN, Soldatova AV, Lee SW, Spiro TG, Tebo BM. Mn(II,III) oxidation and MnO2 mineralization by an expressed bacterial multicopper oxidase. Proc Natl Acad Sci U S A 2013; 110:11731-5. [PMID: 23818588 PMCID: PMC3718108 DOI: 10.1073/pnas.1303677110] [Citation(s) in RCA: 95] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Reactive Mn(IV) oxide minerals are ubiquitous in the environment and control the bioavailability and distribution of many toxic and essential elements and organic compounds. Their formation is thought to be dependent on microbial enzymes, because spontaneous Mn(II) to Mn(IV) oxidation is slow. Several species of marine Bacillus spores oxidize Mn(II) on their exosporium, the outermost layer of the spore, encrusting them with Mn(IV) oxides. Molecular studies have identified the mnx (Mn oxidation) genes, including mnxG, encoding a putative multicopper oxidase (MCO), as responsible for this two-electron oxidation, a surprising finding because MCOs only catalyze single-electron transfer reactions. Characterization of the enzymatic mechanism has been hindered by the lack of purified protein. By purifying active protein from the mnxDEFG expression construct, we found that the resulting enzyme is a blue (absorption maximum 590 nm) complex containing MnxE, MnxF, and MnxG proteins. Further, by analyzing the Mn(II)- and (III)-oxidizing activity in the presence of a Mn(III) chelator, pyrophosphate, we found that the complex facilitates both electron transfers from Mn(II) to Mn(III) and from Mn(III) to Mn(IV). X-ray absorption spectroscopy of the Mn mineral product confirmed its similarity to Mn(IV) oxides generated by whole spores. Our results demonstrate that Mn oxidation from soluble Mn(II) to Mn(IV) oxides is a two-step reaction catalyzed by an MCO-containing complex. With the purification of active Mn oxidase, we will be able to uncover its mechanism, broadening our understanding of Mn mineral formation and the bioinorganic capabilities of MCOs.
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Affiliation(s)
- Cristina N. Butterfield
- Division of Environmental and Biomolecular Systems, Institute of Environmental Health, Oregon Health and Science University, Beaverton, OR 97006; and
| | | | - Sung-Woo Lee
- Division of Environmental and Biomolecular Systems, Institute of Environmental Health, Oregon Health and Science University, Beaverton, OR 97006; and
| | - Thomas G. Spiro
- Department of Chemistry, University of Washington, Seattle, WA 98195
| | - Bradley M. Tebo
- Division of Environmental and Biomolecular Systems, Institute of Environmental Health, Oregon Health and Science University, Beaverton, OR 97006; and
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Plathe KL, Lee SW, Tebo BM, Bargar JR, Bernier-Latmani R. Impact of microbial Mn oxidation on the remobilization of bioreduced U(IV). ENVIRONMENTAL SCIENCE & TECHNOLOGY 2013; 47:3606-3613. [PMID: 23484504 DOI: 10.1021/es3036835] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Effects of Mn redox cycling on the stability of bioreduced U(IV) are evaluated here. U(VI) can be biologically reduced to less soluble U(IV) species and the stimulation of biological activity to that end is a salient remediation strategy; however, the stability of these materials in the subsurface environments where they form remains unproven. Manganese oxides are capable of rapidly oxidizing U(IV) to U(VI) in mixed batch systems where the two solid phases are in direct contact. However, it is unknown whether the same oxidation would take place in a porous medium. To probe that question, U(IV) immobilized in agarose gels was exposed to conditions allowing biological Mn(II) oxidation (HEPES buffer, Mn(II), 5% O2 and Bacillus sp. SG-1 spores). Results show the oxidation of U(IV) to U(VI) is due primarily to O2 rather than to MnO2. U(VI) produced is retained within the gel to a greater extent when Mn oxides are present, suggesting the formation of strong surface complexes. The implication for the long-term stability of U in a bioremediated site is that, in the absence of competing ligands, biological Mn(II) oxidation may promote the immobilization of U(VI) produced by the oxidation of U(IV).
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Affiliation(s)
- Kelly L Plathe
- Environmental Microbiology Laboratory, Ecole Polytechnique Federale de Lausanne, Station 6, CH-1015, Lausanne, Switzerland
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Su J, Bao P, Bai T, Deng L, Wu H, Liu F, He J. CotA, a multicopper oxidase from Bacillus pumilus WH4, exhibits manganese-oxidase activity. PLoS One 2013; 8:e60573. [PMID: 23577125 PMCID: PMC3618234 DOI: 10.1371/journal.pone.0060573] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2012] [Accepted: 02/28/2013] [Indexed: 11/19/2022] Open
Abstract
Multicopper oxidases (MCOs) are a family of enzymes that use copper ions as cofactors to oxidize various substrates. Previous research has demonstrated that several MCOs such as MnxG, MofA and MoxA can act as putative Mn(II) oxidases. Meanwhile, the endospore coat protein CotA from Bacillus species has been confirmed as a typical MCO. To study the relationship between CotA and the Mn(II) oxidation, the cotA gene from a highly active Mn(II)-oxidizing strain Bacillus pumilus WH4 was cloned and overexpressed in Escherichia coli strain M15. The purified CotA contained approximately four copper atoms per molecule and showed spectroscopic properties typical of blue copper oxidases. Importantly, apart from the laccase activities, the CotA also displayed substantial Mn(II)-oxidase activities both in liquid culture system and native polyacrylamide gel electrophoresis. The optimum Mn(II) oxidase activity was obtained at 53°C in HEPES buffer (pH 8.0) supplemented with 0.8 mM CuCl2. Besides, the addition of o-phenanthroline and EDTA both led to a complete suppression of Mn(II)-oxidizing activity. The specific activity of purified CotA towards Mn(II) was 0.27 U/mg. The Km, Vmax and kcat values towards Mn(II) were 14.85±1.17 mM, 3.01×10(-6)±0.21 M·min(-1) and 0.32±0.02 s(-1), respectively. Moreover, the Mn(II)-oxidizing activity of the recombinant E. coli strain M15-pQE-cotA was significantly increased when cultured both in Mn-containing K liquid medium and on agar plates. After 7-day liquid cultivation, M15-pQE-cotA resulted in 18.2% removal of Mn(II) from the medium. Furthermore, the biogenic Mn oxides were clearly observed on the cell surfaces of M15-pQE-cotA by scanning electron microscopy. To our knowledge, this is the first report that provides the direct observation of Mn(II) oxidation with the heterologously expressed protein CotA, Therefore, this novel finding not only establishes the foundation for in-depth study of Mn(II) oxidation mechanisms, but also offers a potential biocatalyst for Mn(II) removal.
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Affiliation(s)
- Jianmei Su
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, People’s Republic of China
| | - Peng Bao
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, People’s Republic of China
| | - Tenglong Bai
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, People’s Republic of China
| | - Lin Deng
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, People’s Republic of China
| | - Hui Wu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, People’s Republic of China
| | - Fan Liu
- Key Laboratory of Arable Land Conservation, Ministry of Agriculture, College of Resources and Environment, Huazhong Agricultural University, Wuhan, Hubei, People’s Republic of China
| | - Jin He
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, People’s Republic of China
- * E-mail:
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59
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Abstract
Multicopper blue proteins, composed of several repetitive copper-binding domains similar to one-domain cupredoxin-like proteins, were found in almost all organisms. They are classified into the three different groups, based on their two-, three- or six-domain organization. We found orthologs of chordate six-domain copper-binding proteins in animals, plants, bacteria and archea. The phylogenetic analysis of 183 multicopper blue proteins and their copper-binding sites comparison make us think that all the modern six-domain blue proteins have originated from the common ancestral six-domain protein in the process of gene duplication and copper-binding sites loss as a result of amino acid substitutions.
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60
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Toyoda K, Tebo BM. The effect of Ca 2+ ions and ionic strength on Mn(II) oxidation by spores of the marine Bacillus sp. SG-1. GEOCHIMICA ET COSMOCHIMICA ACTA 2013; 101:1-11. [PMID: 29176910 PMCID: PMC5701786 DOI: 10.1016/j.gca.2012.10.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Manganese(IV) oxides, believed to form primarily through microbial activities, are extremely important mineral phases in marine environments where they scavenge a variety of trace elements and thereby control their distributions. The presence of various ions common in seawater are known to influence Mn oxide mineralogy yet little is known about the effect of these ions on the kinetics of bacterial Mn(II) oxidation and Mn oxide formation. We examined factors affecting bacterial Mn(II) oxidation by spores of the marine Bacillus sp. strain SG-1 in natural and artificial seawater of varying ionic conditions. Ca2+ concentration dramatically affected Mn(II) oxidation, while Mg2+, Sr2+, K+, Na+ and NO3- ions had no effect. The rate of Mn(II) oxidation at 10mM Ca2+ (seawater composition) was four or five times that without Ca2+. The relationship between Ca2+ content and oxidation rate demonstrates that the equilibrium constant is small (on the order of 0.1) and the binding coefficient is 0.5. The pH optimum for Mn(II) oxidation changed depending on the amount of Ca2+ present, suggesting that Ca2+ exerts a direct effect on the enzyme perhaps as a stabilizing bridge between polypeptide components. We also examined the effect of varying concentrations of NaCl or KNO3 (0 mM - 2000 mM) on the kinetics of Mn(II) oxidation in solutions containing 10 mM Ca2+. Mn(II) oxidation was unaffected by changes in ionic strength (I) below 0.2, but it was inhibited by increasing salt concentrations above this value. Our results suggest that the critical coagulation concentration is around 200 mM of salt (I = ca. 0.2), and that the ionic strength of seawater (I > 0.2) accelerates the precipitation of Mn oxides around the spores. Under these conditions, the aggregation of Mn oxides reduces the supply of dissolved O2 and/or Mn2+ and inhibits the Mn(II) -> Mn(III) step controlling the enzymatic oxidation of Mn(II). Our results suggest that the hardness and ionic strength of the aquatic environment at circumneutral pH strongly influences the rate of biologically mediated Mn(II) oxidation.
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Affiliation(s)
- Kazuhiro Toyoda
- Graduate School of Environmental Science, Hokkaido University, Kita-ku, Sapporo, 060-0810 Japan
| | - Bradley M Tebo
- Division of Environmental & Biomolecular Systems, Institute of Environmental Health, Oregon Health & Science University, 20000 NW Walker Rd. Beaverton, OR 97006
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61
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Soldatova AV, Butterfield C, Oyerinde OF, Tebo BM, Spiro TG. Multicopper oxidase involvement in both Mn(II) and Mn(III) oxidation during bacterial formation of MnO(2). J Biol Inorg Chem 2012; 17:1151-8. [PMID: 22892957 PMCID: PMC3743667 DOI: 10.1007/s00775-012-0928-6] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2012] [Accepted: 07/18/2012] [Indexed: 12/19/2022]
Abstract
Global cycling of environmental manganese requires catalysis by bacteria and fungi for MnO(2) formation, since abiotic Mn(II) oxidation is slow under ambient conditions. Genetic evidence from several bacteria indicates that multicopper oxidases (MCOs) are required for MnO(2) formation. However, MCOs catalyze one-electron oxidations, whereas the conversion of Mn(II) to MnO(2) is a two-electron process. Trapping experiments with pyrophosphate (PP), a Mn(III) chelator, have demonstrated that Mn(III) is an intermediate in Mn(II) oxidation when mediated by exosporium from the Mn-oxidizing bacterium Bacillus SG-1. The reaction of Mn(II) depends on O(2) and is inhibited by azide, consistent with MCO catalysis. We show that the subsequent conversion of Mn(III) to MnO(2) also depends on O(2) and is inhibited by azide. Thus, both oxidation steps appear to be MCO-mediated, likely by the same enzyme, which is indicated by genetic evidence to be the MnxG gene product. We propose a model of how the manganese oxidase active site may be organized to couple successive electron transfers to the formation of polynuclear Mn(IV) complexes as precursors to MnO(2) formation.
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Affiliation(s)
- Alexandra V. Soldatova
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195 USA
| | - Cristina Butterfield
- Division of Environmental and Biomolecular Systems, Oregon Health & Science University, 20000 NW Walker Road, Beaverton, Oregon 97006 USA
| | - Oyeyemi F. Oyerinde
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195 USA
| | - Bradley M. Tebo
- Division of Environmental and Biomolecular Systems, Oregon Health & Science University, 20000 NW Walker Road, Beaverton, Oregon 97006 USA
| | - Thomas G. Spiro
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195 USA
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62
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Hasan HA, Abdullah SRS, Kofli NT, Kamarudin SK. Isotherm equilibria of Mn²⁺ biosorption in drinking water treatment by locally isolated Bacillus species and sewage activated sludge. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2012; 111:34-43. [PMID: 22813857 DOI: 10.1016/j.jenvman.2012.06.027] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2010] [Revised: 06/12/2012] [Accepted: 06/18/2012] [Indexed: 06/01/2023]
Abstract
Manganese (Mn(2+)) is one of the inorganic contaminant that causes problem to water treatment and water distribution due to the accumulation on water piping systems. In this study, Bacillus sp. and sewage activated sludge (SAS) were investigated as biosorbents in laboratory-scale experiments. The study showed that Bacillus sp. was a more effective biosorbent than SAS. The experimental data were fitted to the Langmuir (Langmuir-1 & Langmuir-2), Freundlich, Temkin, Dubinin-Radushkevich (D-R) and Redlich-Peterson (R-P) isotherms to obtain the characteristic parameters of each model. Mn(2+) biosorption by Bacillus sp. was found to be significantly better fitted to the Langmuir-1 isotherm than the other isotherms, while the D-R isotherm was the best fit for SAS; i.e., the χ(2) value was smaller than that for the Freundlich, Temkin, and R-P isotherms. According to the evaluation using the Langmuir-1 isotherm, the maximum biosorption capacities of Mn(2+) onto Bacillus sp. and SAS were 43.5 mg Mn(2+)/g biomass and 12.7 mg Mn(2+)/g biomass, respectively. The data fitted using the D-R isotherm showed that the Mn(2+) biosorption processes by both Bacillus sp. and SAS occurred via the chemical ion-exchange mechanism between the functional groups and Mn(2+) ion.
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Affiliation(s)
- Hassimi Abu Hasan
- Department of Chemical and Process Engineering, Faculty of Engineering and Built Environment, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor Darul Ehsan, Malaysia.
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63
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Roden EE, McBeth JM, Blöthe M, Percak-Dennett EM, Fleming EJ, Holyoke RR, Luther GW, Emerson D, Schieber J. The Microbial Ferrous Wheel in a Neutral pH Groundwater Seep. Front Microbiol 2012; 3:172. [PMID: 22783228 PMCID: PMC3390581 DOI: 10.3389/fmicb.2012.00172] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2012] [Accepted: 04/18/2012] [Indexed: 12/16/2022] Open
Abstract
Evidence for microbial Fe redox cycling was documented in a circumneutral pH groundwater seep near Bloomington, Indiana. Geochemical and microbiological analyses were conducted at two sites, a semi-consolidated microbial mat and a floating puffball structure. In situ voltammetric microelectrode measurements revealed steep opposing gradients of O2 and Fe(II) at both sites, similar to other groundwater seep and sedimentary environments known to support microbial Fe redox cycling. The puffball structure showed an abrupt increase in dissolved Fe(II) just at its surface (∼5 cm depth), suggesting an internal Fe(II) source coupled to active Fe(III) reduction. Most probable number enumerations detected microaerophilic Fe(II)-oxidizing bacteria (FeOB) and dissimilatory Fe(III)-reducing bacteria (FeRB) at densities of 102 to 105 cells mL−1 in samples from both sites. In vitro Fe(III) reduction experiments revealed the potential for immediate reduction (no lag period) of native Fe(III) oxides. Conventional full-length 16S rRNA gene clone libraries were compared with high throughput barcode sequencing of the V1, V4, or V6 variable regions of 16S rRNA genes in order to evaluate the extent to which new sequencing approaches could provide enhanced insight into the composition of Fe redox cycling microbial community structure. The composition of the clone libraries suggested a lithotroph-dominated microbial community centered around taxa related to known FeOB (e.g., Gallionella, Sideroxydans, Aquabacterium). Sequences related to recognized FeRB (e.g., Rhodoferax, Aeromonas, Geobacter, Desulfovibrio) were also well-represented. Overall, sequences related to known FeOB and FeRB accounted for 88 and 59% of total clone sequences in the mat and puffball libraries, respectively. Taxa identified in the barcode libraries showed partial overlap with the clone libraries, but were not always consistent across different variable regions and sequencing platforms. However, the barcode libraries provided confirmation of key clone library results (e.g., the predominance of Betaproteobacteria) and an expanded view of lithotrophic microbial community composition.
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Affiliation(s)
- Eric E Roden
- NASA Astrobiology Institute, Department of Geoscience, University of Wisconsin Madison Madison, WI, USA
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Iodide oxidation by a novel multicopper oxidase from the alphaproteobacterium strain Q-1. Appl Environ Microbiol 2012; 78:3941-9. [PMID: 22447601 DOI: 10.1128/aem.00084-12] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Alphaproteobacterium strain Q-1 is able to oxidize iodide (I(-)) to molecular iodine (I(2)) by an oxidase-like enzyme. One of the two isoforms of the iodide-oxidizing enzyme (IOE-II) produced by this strain was excised from a native polyacrylamide gel, eluted, and purified. IOE-II appeared as a single band (51 kDa) and showed significant in-gel iodide-oxidizing activity in sodium dodecyl sulfate-polyacrylamide gel electrophoresis without heat treatment. However, at least two bands with much higher molecular masses (150 and 230 kDa) were observed with heat treatment (95°C, 3 min). IOE-II was inhibited by NaN(3), KCN, EDTA, and a copper chelator, o-phenanthroline. In addition to iodide, IOE-II showed significant activities toward phenolic compounds such as syringaldazine, 2,6-dimethoxy phenol, and p-phenylenediamine. IOE-II contained copper atoms as prosthetic groups and had UV/VIS absorption peaks at 320 and 590 nm. Comparison of several internal amino acid sequences obtained from trypsin-digested IOE-II with a draft genome sequence of strain Q-1 revealed that the products of two open reading frames (IoxA and IoxC), with predicted molecular masses of 62 and 71 kDa, are involved in iodide oxidation. Furthermore, subsequent tandem mass spectrometric analysis repeatedly detected peptides from IoxA and IoxC with high sequence coverage (32 to 40%). IoxA showed homology with the family of multicopper oxidases and included four copper-binding regions that are highly conserved among various multicopper oxidases. These results suggest that IOE-II is a multicopper oxidase and that it may occur as a multimeric complex in which at least two proteins (IoxA and IoxC) are associated.
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65
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Segev E, Smith Y, Ben-Yehuda S. RNA dynamics in aging bacterial spores. Cell 2011; 148:139-49. [PMID: 22209493 DOI: 10.1016/j.cell.2011.11.059] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2011] [Revised: 09/13/2011] [Accepted: 11/30/2011] [Indexed: 12/21/2022]
Abstract
Upon starvation, the bacterium Bacillus subtilis enters the process of sporulation, lasting several hours and culminating in formation of a spore, the most resilient cell type known. We show that a few days following sporulation, the RNA profile of spores is highly dynamic. In aging spores incubated at high temperatures, RNA content is globally decreased by degradation over several days. This degradation might be a strategy utilized by the spore to facilitate its dormancy. However, spores kept at low temperature exhibit a different RNA profile with evidence supporting transcription. Further, we demonstrate that germination is affected by spore age, incubation temperature, and RNA state, implying that spores can acquire dissimilar characteristics at a time they are considered dormant. We propose that, in contrast to current thinking, entering dormancy lasts a few days, during which spores are affected by the environment and undergo corresponding molecular changes influencing their emergence from quiescence.
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Affiliation(s)
- Einat Segev
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada (IMRIC), The Hebrew University-Hadassah Medical School, The Hebrew University of Jerusalem, 91120 Jerusalem, Israel
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66
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Phelan RW, O'Halloran JA, Kennedy J, Morrissey JP, Dobson ADW, O'Gara F, Barbosa TM. Diversity and bioactive potential of endospore-forming bacteria cultured from the marine sponge Haliclona simulans. J Appl Microbiol 2011; 112:65-78. [PMID: 21985154 DOI: 10.1111/j.1365-2672.2011.05173.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
AIMS Despite the frequent isolation of endospore-formers from marine sponges, little is known about the diversity and characterization of individual isolates. The main aims of this study were to isolate and characterize the spore-forming bacteria from the marine sponge Haliclona simulans and to examine their potential as a source for bioactive compounds. METHODS AND RESULTS A bank of presumptive aerobic spore-forming bacteria was isolated from the marine sponge H. simulans. These represented c. 1% of the total culturable bacterial population. A subgroup of thirty isolates was characterized using morphological, phenotypical and phylogenetic analysis. A large diversity of endospore-forming bacteria was present, with the thirty isolates being distributed through a variety of Bacillus and Paenibacillus species. These included ubiquitous species, such as B. subtilis, B. pumilus, B. licheniformis and B. cereus group, as well as species that are typically associated with marine habitats, such as B. aquimaris, B. algicola and B. hwajinpoensis. Two strains carried the aiiA gene that encodes a lactonase known to be able to disrupt quorum-sensing mechanisms, and various isolates demonstrated protease activity and antimicrobial activity against different pathogenic indicator strains, including Clostridium perfringens, Bacillus cereus and Listeria monocytogenes. CONCLUSIONS The marine sponge H. simulans harbours a diverse collection of endospore-forming bacteria, which produce proteases and antibiotics. This diversity appears to be overlooked by culture-dependent and culture-independent methods that do not specifically target sporeformers. SIGNIFICANCE AND IMPACT OF STUDY Marine sponges are an as yet largely untapped and poorly understood source of endospore-forming bacterial diversity with potential biotechnological, biopharmaceutical and probiotic applications. These results also indicate the importance of combining different methodologies for the comprehensive characterization of complex microbial populations such as those found in marine sponges.
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Affiliation(s)
- R W Phelan
- Department of Microbiology, University College Cork, Cork, Ireland
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67
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Synthesis and characterization of a novel extracellular biogenic manganese oxide (bixbyite-like Mn₂O₃) nanoparticle by isolated Acinetobacter sp. Curr Microbiol 2011; 63:300-5. [PMID: 21761221 DOI: 10.1007/s00284-011-9971-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2011] [Accepted: 06/15/2011] [Indexed: 10/18/2022]
Abstract
Recently, manganese oxides have been considered in the environmental remediation, MRI diagnosis and drug and pharmaceutical industries. Different numbers of physicochemical and biological methods have been reported for the preparation of nanoscale manganese oxides. Although manganese oxide biogenesis by bacterial species has been recognized as the major Mn-oxidizing agent in nature, in this research, for first time, we demonstrated the process which used to produce bixbyite-like Mn(2)O(3) nanoparticles by isolated aerobic bacterium from Persian Gulf water. The 16SRNA sequencing showed that this isolate belong to a gram-negative Acinetobacter which produced nano Mn-oxide crystal particle. Characterization of complement morphology, size and chemical structure of these particles were determined by TEM, SEM, EDAX, XRD and FTIR. The data showed that this bacterium could produce nanosized extracellular bixbyite-like Mn(2)O(3) which depend on enzymatic pathway.
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Manganese Oxidation by Bacteria: Biogeochemical Aspects. MOLECULAR BIOMINERALIZATION 2011; 52:49-76. [DOI: 10.1007/978-3-642-21230-7_3] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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69
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Wang X, Wiens M, Divekar M, Grebenjuk VA, Schröder HC, Batel R, Müller WEG. Isolation and characterization of a Mn(II)-oxidizing Bacillus strain from the demosponge Suberites domuncula. Mar Drugs 2010; 9:1-28. [PMID: 21339943 PMCID: PMC3039467 DOI: 10.3390/md9010001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2010] [Revised: 12/17/2010] [Accepted: 12/22/2010] [Indexed: 11/16/2022] Open
Abstract
In this study we demonstrate that the demosponge Suberites domuncula harbors a Mn(II)-oxidizing bacterium, a Bacillus strain, termed BAC-SubDo-03. Our studies showed that Mn(II) stimulates bacterial growth and induces sporulation. Moreover, we show that these bacteria immobilize manganese on their cell surface. Comparison of the 16S rDNA sequence allowed the grouping of BAC-SubDo-03 to the Mn-precipitating bacteria. Analysis of the spore cell wall revealed that it contains an Mn(II)-oxidizing enzyme. Co-incubation studies of BAC-SubDo-03 with 100 μM MnCl2 and >1 μM of CuCl2 showed an increase in their Mn(II)-oxidizing capacity. In order to prove that a multicopper oxidase-like enzyme(s) (MCO) exists in the cell wall of the S. domuncula-associated BAC-SubDo-03 Bacillus strain, the gene encoding this enzyme was cloned (mnxG-SubDo-03). Sequence alignment of the deduced MCO protein (MnxG-SubDo-03) revealed that the sponge bacterium clusters together with known Mn(II)-oxidizing bacteria. The expression of the mnxG-SubDo-03 gene is under strong control of extracellular Mn(II). Based on these findings, we assume that BAC-SubDo-03 might serve as a Mn reserve in the sponge providing the animal with the capacity to detoxify Mn in the environment. Applying the in vitro primmorph cell culture system we could demonstrate that sponge cells, that were co-incubated with BAC-SubDo-03 in the presence of Mn(II), show an increased proliferation potential.
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Affiliation(s)
- Xiaohong Wang
- National Research Center for Geoanalysis, 26 Baiwanzhuang Dajie, CHN-100037 Beijing, China
- Institute for Physiological Chemistry, Dept. for Applied Molecular Biology, Johannes Gutenberg-University Medical Center, Duesbergweg 6, D-55099 Mainz, Germany; E-Mails: (M.W.); (M.D.); (V.A.G.); (H.C.S.)
- Authors to whom correspondence should be addressed; E-Mails: (X.W.); (W.E.G.M.); Tel.: +49-6131-39-25910; Fax: +49-6131-39-25243
| | - Matthias Wiens
- Institute for Physiological Chemistry, Dept. for Applied Molecular Biology, Johannes Gutenberg-University Medical Center, Duesbergweg 6, D-55099 Mainz, Germany; E-Mails: (M.W.); (M.D.); (V.A.G.); (H.C.S.)
| | - Mugdha Divekar
- Institute for Physiological Chemistry, Dept. for Applied Molecular Biology, Johannes Gutenberg-University Medical Center, Duesbergweg 6, D-55099 Mainz, Germany; E-Mails: (M.W.); (M.D.); (V.A.G.); (H.C.S.)
| | - Vladislav A. Grebenjuk
- Institute for Physiological Chemistry, Dept. for Applied Molecular Biology, Johannes Gutenberg-University Medical Center, Duesbergweg 6, D-55099 Mainz, Germany; E-Mails: (M.W.); (M.D.); (V.A.G.); (H.C.S.)
| | - Heinz C. Schröder
- Institute for Physiological Chemistry, Dept. for Applied Molecular Biology, Johannes Gutenberg-University Medical Center, Duesbergweg 6, D-55099 Mainz, Germany; E-Mails: (M.W.); (M.D.); (V.A.G.); (H.C.S.)
| | - Renato Batel
- Center for Marine Research, “Ruder Boskovic” Institute, HR-52210 Rovinj, Croatia; E-Mail: (R.B.)
| | - Werner E. G. Müller
- Institute for Physiological Chemistry, Dept. for Applied Molecular Biology, Johannes Gutenberg-University Medical Center, Duesbergweg 6, D-55099 Mainz, Germany; E-Mails: (M.W.); (M.D.); (V.A.G.); (H.C.S.)
- Authors to whom correspondence should be addressed; E-Mails: (X.W.); (W.E.G.M.); Tel.: +49-6131-39-25910; Fax: +49-6131-39-25243
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Santelli CM, Pfister DH, Lazarus D, Sun L, Burgos WD, Hansel CM. Promotion of Mn(II) oxidation and remediation of coal mine drainage in passive treatment systems by diverse fungal and bacterial communities. Appl Environ Microbiol 2010; 76:4871-5. [PMID: 20495049 PMCID: PMC2901711 DOI: 10.1128/aem.03029-09] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2009] [Accepted: 05/09/2010] [Indexed: 11/20/2022] Open
Abstract
Biologically active, passive treatment systems are commonly employed for removing high concentrations of dissolved Mn(II) from coal mine drainage (CMD). Studies of microbial communities contributing to Mn attenuation through the oxidation of Mn(II) to sparingly soluble Mn(III/IV) oxide minerals, however, have been sparse to date. This study reveals a diverse community of Mn(II)-oxidizing fungi and bacteria existing in several CMD treatment systems.
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MESH Headings
- Bacteria/classification
- Bacteria/genetics
- Bacteria/metabolism
- Cluster Analysis
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Fungal/chemistry
- DNA, Fungal/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Fungi/classification
- Fungi/genetics
- Fungi/metabolism
- Manganese/metabolism
- Molecular Sequence Data
- Oxidation-Reduction
- Phylogeny
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 18S/genetics
- Sequence Analysis, DNA
- Water Pollutants/metabolism
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Affiliation(s)
- Cara M. Santelli
- Harvard School of Engineering and Applied Sciences, Cambridge, Massachusetts, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, Department of Civil and Environmental Engineering, the Pennsylvania State University, University Park, Pennsylvania
| | - Donald H. Pfister
- Harvard School of Engineering and Applied Sciences, Cambridge, Massachusetts, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, Department of Civil and Environmental Engineering, the Pennsylvania State University, University Park, Pennsylvania
| | - Dana Lazarus
- Harvard School of Engineering and Applied Sciences, Cambridge, Massachusetts, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, Department of Civil and Environmental Engineering, the Pennsylvania State University, University Park, Pennsylvania
| | - Lu Sun
- Harvard School of Engineering and Applied Sciences, Cambridge, Massachusetts, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, Department of Civil and Environmental Engineering, the Pennsylvania State University, University Park, Pennsylvania
| | - William D. Burgos
- Harvard School of Engineering and Applied Sciences, Cambridge, Massachusetts, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, Department of Civil and Environmental Engineering, the Pennsylvania State University, University Park, Pennsylvania
| | - Colleen M. Hansel
- Harvard School of Engineering and Applied Sciences, Cambridge, Massachusetts, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, Department of Civil and Environmental Engineering, the Pennsylvania State University, University Park, Pennsylvania
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Abstract
Microorganisms control the redox cycling of manganese in the natural environment. Although the homogeneous oxidation of Mn(II) to form manganese oxide minerals is slow, solid MnO(2) is the stable form of manganese in the oxygenated portion of the biosphere. Diverse bacteria and fungi have evolved the ability to catalyze this process, producing the manganese oxides found in soils and sediments. Other bacteria have evolved to utilize MnO(2) as a terminal electron acceptor in respiration. This Account summarizes the properties of Mn oxides produced by bacteria (bacteriogenic MnO(2)) and our current thinking about the biochemical mechanisms of bacterial Mn(II) oxidation. According to X-ray absorption spectroscopy and X-ray scattering studies, the MnO(2) produced by bacteria consists of stacked hexagonal sheets of MnO(6) octahedra, but these particles are extremely small and have numerous structural defects, particularly cation vacancies. The defects provide coordination sites for binding exogenous metal ions, which can be adsorbed to a high loading. As a result, bacterial production of MnO(2) influences the bioavailability of these metals in the natural environment. Because of its high surface area and oxidizing power, bacteriogenic MnO(2) efficiently degrades biologically recalcitrant organic molecules to lower-molecular-mass compounds, spurring interest in using these properties in the bioremediation of xenobiotic organic compounds. Finally, bacteriogenic MnO(2) is reduced to soluble Mn(II) rapidly in the presence of exogenous ligands or sunlight. It can therefore help to regulate the bioavailability of Mn(II), which is known to protect organisms from superoxide radicals and is required to assemble the water-splitting complex in photosynthetic organisms. Bioinorganic chemists and microbiologists have long been interested in the biochemical mechanism of Mn(IV) oxide production. The reaction requires a two-electron oxidation of Mn(II), but genetic and biochemical evidence for several bacteria implicate multicopper oxidases (MCOs), which are only known to engage one-electron transfers from substrate to O(2). In experiments with the exosporium of a Mn(II)-oxidizing Bacillus species, we could trap the one-electron oxidation product, Mn(III), as a pyrophosphate complex in an oxygen-dependent reaction inhibited by azide, consistent with MCO catalysis. The Mn(III) pyrophosphate complex can further act as a substrate, reacting in the presence of the exosporium to produce Mn(IV) oxide. Although this process appears to be unprecedented in biology, it is reminiscent of the oxidation of Fe(II) to form Fe(2)O(3) in the ferritin iron storage protein. However, it includes a critical additional step of Mn(III) oxidation or disproportionation. We shall continue to investigate this biochemically unique process with purified enzymes.
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Affiliation(s)
- Thomas G. Spiro
- Department of Chemistry, University of Washington, Seattle, Washington 98195
| | - John R. Bargar
- Stanford Synchrotron Radiation Lightsource, 2575 Sand Hill Road, Menlo Park, California 94025
| | - Garrison Sposito
- Department of Environmental Science, Policy and Management, University of California, Berkeley, California 94720-3114
| | - Bradley M. Tebo
- Division of Environmental and Biomolecular Systems, Oregon Health & Science University, 20000 NW Walker Road, Beaverton, Oregon 97006
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Importance of Extracellular Enzymes for Biogeochemical Processes in Temporary River Sediments during Fluctuating Dry–Wet Conditions. SOIL ENZYMOLOGY 2010. [DOI: 10.1007/978-3-642-14225-3_6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Kosman DJ. Multicopper oxidases: a workshop on copper coordination chemistry, electron transfer, and metallophysiology. J Biol Inorg Chem 2009; 15:15-28. [PMID: 19816718 DOI: 10.1007/s00775-009-0590-9] [Citation(s) in RCA: 125] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2009] [Accepted: 09/15/2009] [Indexed: 01/01/2023]
Abstract
Multicopper oxidases (MCOs) are unique among copper proteins in that they contain at least one each of the three types of biologic copper sites, type 1, type 2, and the binuclear type 3. MCOs are descended from the family of small blue copper proteins (cupredoxins) that likely arose as a complement to the heme-iron-based cytochromes involved in electron transport; this event corresponded to the aerobiosis of the biosphere that resulted in the conversion of Fe(II) to Fe(III) as the predominant redox state of this essential metal and the solubilization of copper from Cu(2)S to Cu(H(2)O)( n ) (2+). MCOs are encoded in genomes in all three kingdoms and play essential roles in the physiology of essentially all aerobes. With four redox-active copper centers, MCOs share with terminal copper-heme oxidases the ability to catalyze the four-electron reduction of O(2) to two molecules of water. The electron transfers associated with this reaction are both outer and inner sphere in nature and their mechanisms have been fairly well established. A subset of MCO proteins exhibit specificity for Fe(2+), Cu(+), and/or Mn(2+) as reducing substrates and have been designated as metallooxidases. These enzymes, in particular the ferroxidases found in all fungi and metazoans, play critical roles in the metal metabolism of the expressing organism.
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Affiliation(s)
- Daniel J Kosman
- Department of Biochemistry, The University at Buffalo, NY 14214, USA.
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Miyata N, Tani Y, Iwahori K, Soma M. Enzymatic formation of manganese oxides by an Acremonium-like hyphomycete fungus, strain KR21-2. FEMS Microbiol Ecol 2009; 47:101-9. [PMID: 19712351 DOI: 10.1016/s0168-6496(03)00251-4] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
A Mn-depositing fungus, Acremonium-like hyphomycete strain KR21-2, was isolated from a Mn deposit occurring on the wall of a storage bottle containing Mn(III, IV) oxide-coated streambed pebbles and stream water. 18S rRNA gene sequence analysis revealed that strain KR21-2 was phylogenetically related to members of the order Hypocreales within the class Ascomycetes. The spent culture medium at the stationary phase of fungal growth contained a 54-kDa protein capable of depositing Mn oxides. The enzymatic activity was inhibited by azide and o-phenanthroline. The Mn(II)-oxidizing protein possessed a laccase activity, as indicated by direct oxidation of p-phenylenediamine and 2,2'-azinobis(3-ethylbenzothiazoline-6-sulfonic acid). These results are consistent with the role assumed for laccase-like multicopper oxidase, which is proposed to be involved in the Mn(II)-oxidizing factors from some bacteria. Unlike laccases of basidiomycete fungi, however, the protein of strain KR21-2 did not produce soluble Mn(III) species in the presence of either of the Mn chelators pyrophosphate and malonate. This is the first report on the possible involvement of laccase and/or multicopper oxidase in Mn oxide deposition by ascomycetes (including their anamorphs) ubiquitous in natural environments.
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Affiliation(s)
- Naoyuki Miyata
- Institute for Environmental Sciences, University of Shizuoka, Yada, Japan.
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Junier P, Frutschi M, Wigginton NS, Schofield EJ, Bargar JR, Bernier-Latmani R. Metal reduction by spores of Desulfotomaculum reducens. Environ Microbiol 2009; 11:3007-17. [PMID: 19601961 DOI: 10.1111/j.1462-2920.2009.02003.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The bioremediation of uranium-contaminated sites is designed to stimulate the activity of microorganisms able to catalyze the reduction of soluble U(VI) to the less soluble mineral UO(2). U(VI) reduction does not necessarily support growth in previously studied bacteria, but it typically involves viable vegetative cells and the presence of an appropriate electron donor. We characterized U(VI) reduction by the sulfate-reducing bacterium Desulfotomaculum reducens strain MI-1 grown fermentatively on pyruvate and observed that spores were capable of U(VI) reduction. Hydrogen gas - a product of pyruvate fermentation - rather than pyruvate, served as the electron donor. The presence of spent growth medium was required for the process, suggesting that an unknown factor produced by the cells was necessary for reduction. Ultrafiltration of the spent medium followed by U(VI) reduction assays revealed that the factor's molecular size was below 3 kDa. Pre-reduced spent medium displayed short-term U(VI) reduction activity, suggesting that the missing factor may be an electron shuttle, but neither anthraquinone-2,6-disulfonic acid nor riboflavin rescued spore activity in fresh medium. Spores of D. reducens also reduced Fe(III)-citrate under experimental conditions similar to those for U(VI) reduction. This is the first report of a bacterium able to reduce metals while in a sporulated state and underscores the novel nature of the mechanism of metal reduction by strain MI-1.
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Affiliation(s)
- Pilar Junier
- Environmental Microbiology Laboratory, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, CH 1015, Switzerland
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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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Anderson CR, Dick GJ, Chu ML, Cho JC, Davis RE, Bräuer SL, Tebo BM. Aurantimonas manganoxydans, sp. nov. and Aurantimonas litoralis, sp. nov.: Mn(II) oxidizing representatives of a globally distributed clade of alpha-Proteobacteria from the order Rhizobiales. GEOMICROBIOLOGY JOURNAL 2009; 26:189-198. [PMID: 19768133 PMCID: PMC2746641 DOI: 10.1080/01490450902724840] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Several closely related Mn(II)-oxidizing alpha-Proteobacteria were isolated from very different marine environments: strain SI85-9A1 from the oxic/anoxic interface of a stratified Canadian fjord, strain HTCC 2156 from the surface waters off the Oregon coast, and strain AE01 from the dorsal surface of a hydrothermal vent tubeworm. 16S rRNA analysis reveals that these isolates are part of a tight phylogenetic cluster with previously characterized members of the genus Aurantimonas. Other organisms within this clade have been isolated from disparate environments such as surface waters of the Arctic and Mediterranean seas, a deep-sea hydrothermal plume, and a Caribbean coral. Further analysis of all these strains revealed that many of them are capable of oxidizing dissolved Mn(II) and producing particulate Mn(III/IV) oxides. Strains SI85-9A1 and HTCC 2156 were characterized further. Despite sharing nearly identical 16S rRNA gene sequences with the previously described Aurantimonas coralicida, whole genome DNA-DNA hybridization indicated that their overall genomic similarity is low. Polyphasic phenotype characterization further supported distinguishing characteristics among these bacteria. Thus SI85-9A1 and HTCC 2156 are described as two new species within the family 'Aurantimionadaceae': Aurantimonas manganoxydans sp. nov. and Aurantimonas litoralis sp. nov. This clade of bacteria is widely distributed around the globe and may be important contributors to Mn cycling in many environments. Our results highlight the difficulty in utilizing 16S rRNA-based approaches to investigate the microbial ecology of Mn(II) oxidation.
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Affiliation(s)
- C. R. Anderson
- Division of Environmental and Biomolecular Systems, Oregon Health and Science University, 20000 NW Walker Road, Beaverton, OR, 97006, USA, Telephone: 503 748 1992, Fax: 503 748 1464
| | - G. J. Dick
- Dept of Geological Sciences, University of Michigan, 2534 CC Little Bldg, 1100 North University Ave, Ann Arbor, MI 48109-1005
| | - M-L. Chu
- Division of Environmental and Biomolecular Systems, Oregon Health and Science University, 20000 NW Walker Road, Beaverton, OR, 97006, USA, Telephone: 503 748 1992, Fax: 503 748 1464
| | - J-C. Cho
- Department of Ocean Sciences, Division of Biology and Ocean Sciences, Inha University, Incheon 402-751, Republic of Korea
| | - R. E. Davis
- Division of Environmental and Biomolecular Systems, Oregon Health and Science University, 20000 NW Walker Road, Beaverton, OR, 97006, USA, Telephone: 503 748 1992, Fax: 503 748 1464
| | - S. L. Bräuer
- Rankin Science South, Appalachian State University, 572 Rivers Street, Boone, NC 28608-2027
| | - B. M. Tebo
- Division of Environmental and Biomolecular Systems, Oregon Health and Science University, 20000 NW Walker Road, Beaverton, OR, 97006, USA, Telephone: 503 748 1992, Fax: 503 748 1464
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78
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Hennebel T, De Gusseme B, Boon N, Verstraete W. Biogenic metals in advanced water treatment. Trends Biotechnol 2009; 27:90-8. [DOI: 10.1016/j.tibtech.2008.11.002] [Citation(s) in RCA: 140] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2008] [Revised: 10/31/2008] [Accepted: 11/03/2008] [Indexed: 10/21/2022]
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79
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Lewandowski Z, Beyenal H. Mechanisms of Microbially Influenced Corrosion. MARINE AND INDUSTRIAL BIOFOULING 2008. [DOI: 10.1007/978-3-540-69796-1_3] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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80
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Phylogenetic Relationships and Functional Genes: Distribution of a Gene (mnxG) encoding a putative manganese-oxidizing enzyme in Bacillus species. Appl Environ Microbiol 2008; 74:7265-71. [PMID: 18849460 DOI: 10.1128/aem.00540-08] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Several Bacillus and Paenibacillus species were isolated from Fe and Mn oxide minerals precipitating at a deep subsurface oxic-anoxic interface at Henderson Molybdenum Mine, Empire, CO. The isolates were investigated for their Mn(II)-oxidizing potential and interrogated for possession of the mnxG gene, a gene that codes for a putative Mn(II)-oxidizing enzyme in Bacillus species. Seven of eight Bacillus species were capable of Mn(II) oxidation; however, the mnxG gene was detected in only one isolate. Using sequences of known Bacillus species both with and without amplifiable mnxG genes and Henderson Mine isolates, the 16S rRNA and mnxG gene phylogenies were compared to determine if 16S rRNA sequences could be used to predict the presence or absence of an amplifiable mnxG gene within the genomes of the isolates. We discovered a strong correspondence between 16S rRNA sequence similarity and the presence/absence of an amplifiable mnxG gene in the isolates. The data revealed a complex phylogenetic distribution of the mnxG gene in which vertical inheritance and gene loss influence the distribution of the gene among the Bacillus species included in this study. Comparisons of 16S rRNA and functional gene phylogenies can be used as a tool to aid in unraveling the history and dispersal of the mnxG gene within the Bacillus clade.
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81
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Dick GJ, Podell S, Johnson HA, Rivera-Espinoza Y, Bernier-Latmani R, McCarthy JK, Torpey JW, Clement BG, Gaasterland T, Tebo BM. Genomic insights into Mn(II) oxidation by the marine alphaproteobacterium Aurantimonas sp. strain SI85-9A1. Appl Environ Microbiol 2008; 74:2646-58. [PMID: 18344346 PMCID: PMC2394881 DOI: 10.1128/aem.01656-07] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2007] [Accepted: 03/02/2008] [Indexed: 01/06/2023] Open
Abstract
Microbial Mn(II) oxidation has important biogeochemical consequences in marine, freshwater, and terrestrial environments, but many aspects of the physiology and biochemistry of this process remain obscure. Here, we report genomic insights into Mn(II) oxidation by the marine alphaproteobacterium Aurantimonas sp. strain SI85-9A1, isolated from the oxic/anoxic interface of a stratified fjord. The SI85-9A1 genome harbors the genetic potential for metabolic versatility, with genes for organoheterotrophy, methylotrophy, oxidation of sulfur and carbon monoxide, the ability to grow over a wide range of O(2) concentrations (including microaerobic conditions), and the complete Calvin cycle for carbon fixation. Although no growth could be detected under autotrophic conditions with Mn(II) as the sole electron donor, cultures of SI85-9A1 grown on glycerol are dramatically stimulated by addition of Mn(II), suggesting an energetic benefit from Mn(II) oxidation. A putative Mn(II) oxidase is encoded by duplicated multicopper oxidase genes that have a complex evolutionary history including multiple gene duplication, loss, and ancient horizontal transfer events. The Mn(II) oxidase was most abundant in the extracellular fraction, where it cooccurs with a putative hemolysin-type Ca(2+)-binding peroxidase. Regulatory elements governing the cellular response to Fe and Mn concentration were identified, and 39 targets of these regulators were detected. The putative Mn(II) oxidase genes were not among the predicted targets, indicating that regulation of Mn(II) oxidation is controlled by other factors yet to be identified. Overall, our results provide novel insights into the physiology and biochemistry of Mn(II) oxidation and reveal a genome specialized for life at the oxic/anoxic interface.
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Affiliation(s)
- Gregory J Dick
- Department of Environmental and Biomolecular Systems, OGI School of Science & Engineering, Oregon Health & Sciences University, 20000 NW Walker Rd., Beaverton, OR 97006, USA
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82
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Direct identification of a bacterial manganese(II) oxidase, the multicopper oxidase MnxG, from spores of several different marine Bacillus species. Appl Environ Microbiol 2007; 74:1527-34. [PMID: 18165363 DOI: 10.1128/aem.01240-07] [Citation(s) in RCA: 117] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Microorganisms catalyze the formation of naturally occurring Mn oxides, but little is known about the biochemical mechanisms of this important biogeochemical process. We used tandem mass spectrometry to directly analyze the Mn(II)-oxidizing enzyme from marine Bacillus spores, identified as an Mn oxide band with an in-gel activity assay. Nine distinct peptides recovered from the Mn oxide band of two Bacillus species were unique to the multicopper oxidase MnxG, and one peptide was from the small hydrophobic protein MnxF. No other proteins were detected in the Mn oxide band, indicating that MnxG (or a MnxF/G complex) directly catalyzes biogenic Mn oxide formation. The Mn(II) oxidase was partially purified and found to be resistant to many proteases and active even at high concentrations of sodium dodecyl sulfate. Comparative analysis of the genes involved in Mn(II) oxidation from three diverse Bacillus species revealed a complement of conserved Cu-binding regions not present in well-characterized multicopper oxidases. Our results provide the first direct identification of a bacterial enzyme that catalyzes Mn(II) oxidation and suggest that MnxG catalyzes two sequential one-electron oxidations from Mn(II) to Mn(III) and from Mn(III) to Mn(IV), a novel type of reaction for a multicopper oxidase.
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83
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Murray KJ, Webb SM, Bargar JR, Tebo BM. Indirect oxidation of Co(II) in the presence of the marine Mn(II)-oxidizing bacterium Bacillus sp. strain SG-1. Appl Environ Microbiol 2007; 73:6905-9. [PMID: 17827312 PMCID: PMC2074982 DOI: 10.1128/aem.00971-07] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2007] [Accepted: 08/30/2007] [Indexed: 11/20/2022] Open
Abstract
Cobalt(II) oxidation in aquatic environments has been shown to be linked to Mn(II) oxidation, a process primarily mediated by bacteria. This work examines the oxidation of Co(II) by the spore-forming marine Mn(II)-oxidizing bacterium Bacillus sp. strain SG-1, which enzymatically catalyzes the formation of reactive nanoparticulate Mn(IV) oxides. Preparations of these spores were incubated with radiotracers and various amounts of Co(II) and Mn(II), and the rates of Mn(II) and Co(II) oxidation were measured. Inhibition of Mn(II) oxidation by Co(II) and inhibition of Co(II) oxidation by Mn(II) were both found to be competitive. However, from both radiotracer experiments and X-ray spectroscopic measurements, no Co(II) oxidation occurred in the complete absence of Mn(II), suggesting that the Co(II) oxidation observed in these cultures is indirect and that a previous report of enzymatic Co(II) oxidation may have been due to very low levels of contaminating Mn. Our results indicate that the mechanism by which SG-1 oxidizes Co(II) is through the production of the reactive nanoparticulate Mn oxide.
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Affiliation(s)
- Karen J Murray
- Scripps Institution of Oceanography, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0202, USA
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84
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Species-level identification of Bacillus strains isolates from marine sediments by conventional biochemical, 16S rRNA gene sequencing and inter-tRNA gene sequence lengths analysis. Antonie van Leeuwenhoek 2007; 93:297-304. [PMID: 17922298 DOI: 10.1007/s10482-007-9204-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2007] [Accepted: 09/20/2007] [Indexed: 10/22/2022]
Abstract
The aim of this study was to compare the ability of commonly used conventional biochemical tests, sequencing analysis of 16S rRNA genes and tDNA-intergenic spacer length polymorphism (tDNA-PCR) to identify species of the genus Bacillus recovered from marine sediments. While biochemical tests were not sufficiently sensitive to distinguish between the 23 marine strains analyzed, partial 16S rRNA gene sequences allowed a correct identification, clustering them into four species belonging to Bacillus licheniformis (n = 6), Bacillus cereus (n = 9), Bacillus subtilis (n = 7) and Bacillus pumilus (n = 1). The identification results obtained with 16S rRNA sequencing were validated by tDNA-PCR analysis of 23 marine isolates that were identified by the similarities of their fingerprints to those of reference strains. tDNA-PCR fingerprinting was as discriminatory as 16S rRNA sequencing analysis. Although it was not able to distinguish among the species of the B. cereus and B. subtilis groups, it should be considered a rapid and easy approach for the reliable identification of unknown Bacillus isolates or at least for the primary differentiation of Bacillus groups.
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85
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Saratovsky I, Wightman PG, Pastén PA, Gaillard JF, Poeppelmeier KR. Manganese oxides: parallels between abiotic and biotic structures. J Am Chem Soc 2007; 128:11188-98. [PMID: 16925437 DOI: 10.1021/ja062097g] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A large number of microorganisms are responsible for the oxidation of Mn(2+)((aq)) to insoluble Mn(3+/4+) oxides (MnO(x)()) in natural aquatic systems. This paper reports the structure of the biogenic MnO(x)(), including a quantitative analysis of cation vacancies, formed by the freshwater bacterium Leptothrix discophora SP6 (SP6-MnO(x)()). The structure and the morphology of SP6-MnO(x)() were characterized by transmission electron microscopy (TEM), X-ray absorption spectroscopy (XAS), including full multiple-scattering analysis, and powder X-ray diffraction (XRD). The biogenic precipitate consists of nanoparticles that are approximately 10 nm by 100 nm in dimension with a fibrillar morphology that resembles twisted sheets. The results dem-onstrate that this biogenic MnO(x)() is composed of sheets of edge-sharing of Mn(4+)O(6) octahedra that form layers. The detailed analysis of the EXAFS spectra indicate that 12 +/- 4% of the Mn(4+) layer cation sites in SP6-MnO(x)() are vacant, whereas the analysis of the XANES suggests that the average oxidation state of Mn is 3.8 +/- 0.3. Therefore, the average chemical formula of SP6-MnO(x)() is M(n)()(+)(y)()Mn(3+)(0.12)[ square(0.12)Mn(4+)(0.88)]O(2).zH(2)O, where M(n)()(+)(y)() represents hydrated interlayer cations, square(0.12) represents Mn(4+) cation vacancies within the layer, and Mn(3+)(0.12) represents hydrated cations that occupy sites above/below these cation vacancies.
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Affiliation(s)
- Ian Saratovsky
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, USA
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86
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Quintanar L, Stoj C, Taylor AB, Hart PJ, Kosman DJ, Solomon EI. Shall we dance? How a multicopper oxidase chooses its electron transfer partner. Acc Chem Res 2007; 40:445-52. [PMID: 17425282 DOI: 10.1021/ar600051a] [Citation(s) in RCA: 147] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Multicopper oxidases (MCOs) are encoded in the genomes of Eukarya, Bacteria, and Archea. These proteins are unique in that they contain at least four Cu atom prosthetic groups organized into one each of the three spectral classifications of copper sites in biology: type 1 (T1), type 2 (T2), and binuclear type 3 (T3), where the T2 and T3 sites form a trinuclear Cu cluster. With these four redox-active copper sites, the multicopper oxidases catalyze the four-electron (4e(-)) reduction of dioxygen to 2H2O, an activity that they alone share with the terminal heme-containing oxidases. Most MCOs exhibit broad specificity towards organic reductants, while a relatively small number of family members exhibit equally robust activity towards metal ions like Fe(II), Cu(I), and Mn(II) and, thus, are considered metallo-oxidases. This Account analyzes the structure-activity features of multicopper oxidases that determine their relative substrate specificity. Since the substrate oxidation step involves an outer-sphere electron transfer from the reductant to the T1Cu site in the protein, the concepts of Marcus theory are applied to unravel the origin of the substrate specificity of the multicopper ferroxidases.
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Affiliation(s)
- Liliana Quintanar
- Centro de Investigación y de Estudios Avanzados, México, D.F., México
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87
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Gontang EA, Fenical W, Jensen PR. Phylogenetic diversity of gram-positive bacteria cultured from marine sediments. Appl Environ Microbiol 2007; 73:3272-82. [PMID: 17400789 PMCID: PMC1907118 DOI: 10.1128/aem.02811-06] [Citation(s) in RCA: 207] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Major advances in our understanding of marine bacterial diversity have been gained through studies of bacterioplankton, the vast majority of which appear to be gram negative. Less effort has been devoted to studies of bacteria inhabiting marine sediments, yet there is evidence to suggest that gram-positive bacteria comprise a relatively large proportion of these communities. To further expand our understanding of the aerobic gram-positive bacteria present in tropical marine sediments, a culture-dependent approach was applied to sediments collected in the Republic of Palau from the intertidal zone to depths of 500 m. This investigation resulted in the isolation of 1,624 diverse gram-positive bacteria spanning 22 families, including many that appear to represent new taxa. Phylogenetic analysis of 189 representative isolates, based on 16S rRNA gene sequence data, indicated that 124 (65.6%) belonged to the class Actinobacteria while the remaining 65 (34.4%) were members of the class Bacilli. Using a sequence identity value of >/=98%, the 189 isolates grouped into 78 operational taxonomic units, of which 29 (37.2%) are likely to represent new taxa. The high degree of phylogenetic novelty observed during this study highlights the fact that a great deal remains to be learned about the diversity of gram-positive bacteria in marine sediments.
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MESH Headings
- Actinobacteria/classification
- Actinobacteria/genetics
- Actinobacteria/growth & development
- Actinobacteria/isolation & purification
- Bacillaceae/classification
- Bacillaceae/genetics
- Bacillaceae/growth & development
- Bacillaceae/isolation & purification
- Biodiversity
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Genes, rRNA
- Geologic Sediments/microbiology
- Gram-Positive Bacteria/classification
- Gram-Positive Bacteria/genetics
- Gram-Positive Bacteria/growth & development
- Gram-Positive Bacteria/isolation & purification
- Molecular Sequence Data
- Palau
- Phylogeny
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
- Water Microbiology
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Affiliation(s)
- Erin A Gontang
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, 9500 Gilman Dr., La Jolla, CA 92093-0204, USA
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88
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Shao Z, Sun F. Intracellular sequestration of manganese and phosphorus in a metal-resistant fungus Cladosporium cladosporioides from deep-sea sediment. Extremophiles 2007; 11:435-43. [PMID: 17265162 DOI: 10.1007/s00792-006-0051-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2006] [Accepted: 11/21/2006] [Indexed: 10/23/2022]
Abstract
A heavy metal resistant fungus was isolated from the sediment of Pacific Ocean, and identified to be Cladosporium cladosporioides. It grew normally in a medium containing 60 mM Mn(2+) and could endure 1,200 mM as the highest concentration tested. Quantification analysis confirmed a high accumulation of Mn which was 58 mg/g in dried biomass. Under transmission electron microscope, many intracellular crystals were observed in the cytoplasm of the hypha cells grown in a Mn-rich medium, and varied from a few nanometers to 200 nm in length. Energy dispersive X-ray (EDX) analysis showed that the crystals were composed of manganese and phosphorus in atomic ratio of 1.6:1 (Mn/P). Further, factors which might influence the resistance of this fungus were investigated. As a result, its high resistance to Mn(2+) was found dependent on the presence of Mg(2+), and could be further enhanced by phosphate. However, the effect of phosphate was not observed without the presence of Mg(2+). In addition, the resistance was also influenced by pH of the medium, which was lost above pH 8. This is the first report on a fungus which showed a hyper resistance to manganese by forming a large quantity of intracellular Mn/P crystals.
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Affiliation(s)
- Zongze Shao
- Key Lab of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, Daxue Road 178#, 361005, Xiamen, Fujian, China.
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89
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Dick GJ, Lee YE, Tebo BM. Manganese(II)-oxidizing Bacillus spores in Guaymas Basin hydrothermal sediments and plumes. Appl Environ Microbiol 2006; 72:3184-90. [PMID: 16672456 PMCID: PMC1472353 DOI: 10.1128/aem.72.5.3184-3190.2006] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Microbial oxidation and precipitation of manganese at deep-sea hydrothermal vents are important oceanic biogeochemical processes, yet nothing is known about the types of microorganisms or mechanisms involved. Here we report isolation of a number of diverse spore-forming Mn(II)-oxidizing Bacillus species from Guaymas Basin, a deep-sea hydrothermal vent environment in the Gulf of California, where rapid microbially mediated Mn(II) oxidation was previously observed. mnxG multicopper oxidase genes involved in Mn(II) oxidation were amplified from all Mn(II)-oxidizing Bacillus spores isolated, suggesting that a copper-mediated mechanism of Mn(II) oxidation could be important at deep-sea hydrothermal vents. Phylogenetic analysis of 16S rRNA and mnxG genes revealed that while many of the deep-sea Mn(II)-oxidizing Bacillus species are very closely related to previously recognized isolates from coastal sediments, other organisms represent novel strains and clusters. The growth and Mn(II) oxidation properties of these Bacillus species suggest that in hydrothermal sediments they are likely present as spores that are active in oxidizing Mn(II) as it emerges from the seafloor.
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Affiliation(s)
- Gregory J Dick
- Department of Environmental and Biomolecular Systems, OGI School of Science & Engineering, Oregon Health & Sciences University, 20000 NW Walker Road, Beaverton, OR 97006, USA
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90
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Mayr R, Busse HJ, Worliczek HL, Ehling-Schulz M, Scherer S. Ornithinibacillus gen. nov., with the species Ornithinibacillus bavariensis sp. nov. and Ornithinibacillus californiensis sp. nov. Int J Syst Evol Microbiol 2006; 56:1383-1389. [PMID: 16738118 DOI: 10.1099/ijs.0.64038-0] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-positive, aerobic, rod-shaped, motile, endospore-forming bacterium was isolated from pasteurized milk from Bavaria, Germany. 16S rRNA gene sequence similarities indicated that strain WSBC 24001T was most closely related to Virgibacillus species (95.3–96.1 %), Oceanobacillus species (95.6–95.7 %), Bacillus firmus IAM 12464T (95.5 %) and Bacillus niacini IFO 15566T (95.2 %). However, strain WSBC 24001T showed the highest level of sequence similarity to an unnamed strain, MB-9T (97.6 %), which was isolated from coastal surface sediments in California. Hence, this strain was included in our study. The genomic DNA G+C contents of strains WSBC 24001T and MB-9T were 36.4 mol and 40.8 mol%, respectively. The major respiratory quinone of both strains was menaquinone MK-7 and the peptidoglycan type was A4β (l-orn←d-Asp). The polar lipid profiles of these strains contained a predominance of diphosphatidylglycerol and moderate to minor amounts of phosphatidylglycerol, an unknown phospholipid and an unknown aminophospholipid. However, strain WSBC 24001T could be distinguished from strain MB-9T by the presence of an unknown lipid. The fatty acid profiles of the two strains comprised mainly iso- and anteiso-branched acids, but showed some significant quantitative differences in the amounts of certain acids. The DNA–DNA relatedness value (15.5 %) clearly demonstrated that strains WSBC 24001T and MB-9T are representatives of two different species. On the basis of their phylogenetic position and morphological, physiological and chemotaxonomic properties, a novel genus is proposed, Ornithinibacillus gen. nov., with two novel species, the type species Ornithinibacillus bavariensis sp. nov. (type strain WSBC 24001T=DSM 15681T=CCM 7096T) and Ornithinibacillus californiensis sp. nov. (type strain MB-9T=DSM 16628T=CCM 7237T).
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Affiliation(s)
- R Mayr
- Lehrstuhl für Mikrobielle Ökologie, Department für Grundlagen der Biowissenschaften, WZW, Technische Universität München, D-85354 Freising, Germany
| | - H-J Busse
- Institut für Bakteriologie, Mykologie und Hygiene, Veterinärmedizinische Universität, A-1210 Wien, Austria
| | - H L Worliczek
- Institut für Bakteriologie, Mykologie und Hygiene, Veterinärmedizinische Universität, A-1210 Wien, Austria
| | - M Ehling-Schulz
- Lehrstuhl für Mikrobielle Ökologie, Department für Grundlagen der Biowissenschaften, WZW, Technische Universität München, D-85354 Freising, Germany
| | - S Scherer
- Lehrstuhl für Mikrobielle Ökologie, Department für Grundlagen der Biowissenschaften, WZW, Technische Universität München, D-85354 Freising, Germany
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91
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Webb SM, Fuller CC, Tebo BM, Bargar JR. Determination of uranyl incorporation into biogenic manganese oxides using x-ray absorption spectroscopy and scattering. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2006; 40:771-7. [PMID: 16509317 DOI: 10.1021/es051679f] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Biogenic manganese oxides are common and an important source of reactive mineral surfaces in the environment that may be potentially enhanced in bioremediation cases to improve natural attenuation. Experiments were performed in which the uranyl ion, UO2(2+) (U(VI)), at various concentrations was present during manganese oxide biogenesis. At all concentrations, there was strong uptake of U onto the oxides. Synchrotron-based extended X-ray absorption fine structure (EXAFS) spectroscopy and X-ray diffraction (XRD) studies were carried out to determine the molecular-scale mechanism by which uranyl is incorporated into the oxide and how this incorporation affects the resulting manganese oxide structure and mineralogy. The EXAFS experiments show that at low concentrations (<0.3 mol % U, <1 microM U(VI) in solution), U(VI) is present as a strong bidentate surface complex. At high concentrations (>2 mol % U, >4 microM U(VI) in solution), the presence of U(VI) affects the stability and structure of the Mn oxide to form poorly ordered Mn oxide tunnel structures, similar to todorokite. EXAFS modeling shows that uranyl is present in these oxides predominantly in the tunnels of the Mn oxide structure in a tridentate complex. Observations by XRD corroborate these results. Structural incorporation may lead to more stable U(VI) sequestration that may be suitable for remediation uses. These observations, combined with the very high uptake capacity of the Mn oxides, imply that Mn-oxidizing bacteria may significantly influence dissolved U(VI) concentrations in impacted waters via sorption and incorporation into Mn oxide biominerals.
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Affiliation(s)
- S M Webb
- Stanford Synchrotron Radiation Laboratory, Menlo Park, California 94025, USA.
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92
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Fernandes SO, Krishnan KP, Khedekar VD, Loka Bharathi PA. Manganese oxidation by bacterial isolates from the Indian ridge system. Biometals 2005; 18:483-92. [PMID: 16333749 DOI: 10.1007/s10534-005-3000-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2005] [Accepted: 09/07/2005] [Indexed: 10/25/2022]
Abstract
The abundance and activity of culturable manganese-oxidizing bacteria were assessed from near-bottom water samples of the tectonically active Carlsberg Ridge. Retrievable counts as colony forming units (CFU) on dilute nutrient agar medium (dilNA=2 gm l(-1) nutrient broth+2% agar) and on dilNA supplemented with 1, 2 and 3 mM MnCl(2).4H(2)O were in the order of 10(6) CFU l(-1). Retrievability of heterotrophs ranged from non-detectable levels (ND) to 2.82 x 10(6) CFU l(-1). The retrievable counts on Mn amended dilNA ranged from ND to 3.21 x 10(6), 1.47 x 10(6) and 1.45 x 10(6) CFU l(-1) on 1, 2 and 3 mM, respectively. About 87% of the Mn tolerant isolates (n=39) showed taxonomic affinities to Pseudomonas I and II sp. Two representative strains CR35 and CR48 (CR-Carlsberg Ridge) isolated on manganese-supplemented media were tested for their ability to tolerate a range of Mn amendments from 1 nM to 100 mM in terms of growth and respiration. CR35 represents 66% of the total CFU (3.04 x 10(6) CFU l(-1)), while CR48 represented only 6% of the total CFU (1.05 x 10(6) CFU l(-1)). The colonies of these two isolates were dark brown in color suggesting precipitation of Mn as oxide. Tests for the effect on growth and respiration were conducted in media simulating heterotrophic (amended with 0.01% glucose) and lithotrophic (unamended) conditions. Maximum stimulation in growth and respiration of CR35 occurred at 100 microM Mn both in unamended and amended media. At levels of Mn greater than 100 microM the counts decreased steadily. Total respiring cells of CR48 were stimulated to a maximum at 1 microM Mn in unamended medium and 1 nM in amended medium. Total cells counts for the same decreased beyond 100 microM Mn in unamended and 1 nM in amended medium. The isolates were tested for their ability to oxidize Mn amendments from 1 microM to 10 mM Mn. At the end of a 76-day incubation period, there was evidence of manganese oxide precipitation at high Mn concentrations (>or=1 mM) as a dark brown coloration on the sides of culture tubes. Highest Mn oxidation rates were observed at 10 mM Mn(II) concentration with CR35 oxidizing 27 and 25 microM Mn day(-1) in unamended and amended condition, respectively. CR48 oxidized Mn at the rate of 26 microM Mn day(-1) in unamended medium and 35 microM Mn day(-1) in amended medium. Scanning electron microscope (SEM) observations of both isolates revealed free-living cells in clustered matrices approximately 2 microm diameter. Energy dispersive spectrum of the cell matrix of CR35 cultured in 1 mM Mn detected 30% Mn, while the cell aggregates of CR48 harbored 7-10% Mn. The relatively high specific activity of these mixotrophic bacteria under relatively oligotrophic conditions suggests that they may be responsible for scavenging dissolved Mn from the Carlsberg Ridge waters and could potentially participate in oxidation.
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93
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Tebo BM, Johnson HA, McCarthy JK, Templeton AS. Geomicrobiology of manganese(II) oxidation. Trends Microbiol 2005; 13:421-8. [PMID: 16054815 DOI: 10.1016/j.tim.2005.07.009] [Citation(s) in RCA: 277] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2005] [Revised: 05/27/2005] [Accepted: 07/21/2005] [Indexed: 10/25/2022]
Abstract
Mn(II)-oxidizing microbes have an integral role in the biogeochemical cycling of manganese, iron, nitrogen, carbon, sulfur, and several nutrients and trace metals. There is great interest in mechanistically understanding these cycles and defining the importance of Mn(II)-oxidizing bacteria in modern and ancient geochemical environments. Linking Mn(II) oxidation to cellular function, although still enigmatic, continues to drive efforts to characterize manganese biomineralization. Recently, complexed-Mn(III) has been shown to be a transient intermediate in Mn(II) oxidation to Mn(IV), suggesting that the reaction might involve a unique multicopper oxidase system capable of a two-electron oxidation of the substrate. In biogenic and abiotic synthesis experiments, the application of synchrotron-based X-ray scattering and spectroscopic techniques has significantly increased our understanding of the oxidation state and relatively amorphous structure (i.e. delta-MnO(2)-like) of biogenic oxides, providing a new blueprint for the structural signature of biogenic Mn oxides.
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Affiliation(s)
- Bradley M Tebo
- Scripps Institution of Oceanography, University of California-San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0202, USA.
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94
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López-García P, Kazmierczak J, Benzerara K, Kempe S, Guyot F, Moreira D. Bacterial diversity and carbonate precipitation in the giant microbialites from the highly alkaline Lake Van, Turkey. Extremophiles 2005; 9:263-74. [PMID: 15959626 DOI: 10.1007/s00792-005-0457-0] [Citation(s) in RCA: 100] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2004] [Accepted: 10/29/2004] [Indexed: 10/25/2022]
Abstract
Lake Van harbors the largest known microbialites on Earth. The surface of these huge carbonate pinnacles is covered by coccoid cyanobacteria whereas their central axis is occupied by a channel through which neutral, relatively Ca-enriched, groundwater flows into highly alkaline (pH approximately 9.7) Ca-poor lake water. Previous microscopy observations showed the presence of aragonite globules composed by rounded nanostructures of uncertain origin that resemble similar bodies found in some meteorites. Here, we have carried out fine-scale mineralogical and microbial diversity analyses from surface and internal microbialite samples. Electron transmission microscopy revealed that the nanostructures correspond to rounded aragonite nanoprecipitates. A progressive mineralization of cells by the deposition of nanoprecipitates on their surface was observed from external towards internal microbialite areas. Molecular diversity studies based on 16S rDNA amplification revealed the presence of bacterial lineages affiliated to the Alpha-, Beta- and Gammaproteobacteria, the Cyanobacteria, the Cytophaga-Flexibacter-Bacteroides (CFB) group, the Actinobacteria and the Firmicutes. Cyanobacteria and CFB members were only detected in surface layers. The most abundant and diverse lineages were the Firmicutes (low GC Gram positives). To the exclusion of cyanobacteria, the closest cultivated members to the Lake Van phylotypes were most frequently alkaliphilic and/or heterotrophic bacteria able to degrade complex organics. These heterotrophic bacteria may play a crucial role in the formation of Lake Van microbialites by locally promoting carbonate precipitation.
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Affiliation(s)
- Purificación López-García
- Unité d'Ecologie, Systématique et Evolution, UMR CNRS 8079, Université Paris-Sud, Orsay Cedex, France.
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95
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Webb SM, Dick GJ, Bargar JR, Tebo BM. Evidence for the presence of Mn(III) intermediates in the bacterial oxidation of Mn(II). Proc Natl Acad Sci U S A 2005; 102:5558-63. [PMID: 15800042 PMCID: PMC556228 DOI: 10.1073/pnas.0409119102] [Citation(s) in RCA: 154] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2004] [Indexed: 11/18/2022] Open
Abstract
Bacterial oxidation of Mn(II) to Mn(IV) is believed to drive the oxidative segment of the global biogeochemical Mn cycle and regulates the concentration of dissolved Mn(II) in the oceanic water column, where it is a critical nutrient for planktonic primary productivity. Mn(II) oxidizing activity is expressed by numerous phylogenetically diverse bacteria and fungi, suggesting that it plays a fundamental and ubiquitous role in the environment. This important redox system is believed to be driven by an enzyme or enzyme complex involving a multicopper oxidase, although the biochemical mechanism has never been conclusively demonstrated. Here, we show that Mn(II) oxidation by spores of the marine Bacillus sp. strain SG-1 is a result of two sequential one-step electron transfer processes, both requiring the putative multicopper oxidase, MnxG, in which Mn(III) is a transient intermediate. A kinetic model of the oxidation pathway is presented, which shows that the Mn(II) to Mn(III) step is the rate-limiting step. Thus, oxidation of Mn(II) appears to involve a unique multicopper oxidase system capable of the overall two-electron oxidation of its substrate. This enzyme system may serve as a source for environmental Mn(III), a strong oxidant and competitor for siderophore-bound Fe(III) in nutrient-limited environments. That metabolically dormant spores catalyze an important biogeochemical process intimately linked to the C, N, Fe, and S cycles requires us to rethink the role of spores in the environment.
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Affiliation(s)
- Samuel M Webb
- Stanford Synchrotron Radiation Laboratory, Menlo Park, CA 94025, USA
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96
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Tani Y, Miyata N, Ohashi M, Ohnuki T, Seyama H, Iwahori K, Soma M. Interaction of inorganic arsenic with biogenic manganese oxide produced by a Mn-oxidizing fungus, strain KR21-2. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2004; 38:6618-6624. [PMID: 15669320 DOI: 10.1021/es049226i] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
In batch culture experiments we examined oxidation of As(III) and adsorption of As(III/V) by biogenic manganese oxide formed by a manganese oxide-depositing fungus, strain KR21-2. We expected to gain insight into the applicability of Mn-depositing microorganisms for biological treatment of As-contaminated waters. In cultures containing Mn2+ and As(V), the solid Mn phase was rich in bound Mn2+ (molar ratio, approximately 30%) and showed a transiently high accumulation of As(V) during the early stage of manganese oxide formation. As manganese oxide formation progressed, a large proportion of adsorbed As(V) was subsequently released. The high proportion of bound Mn2+ may suppress a charge repulsion between As(V) and the manganese oxide surface, which has structural negative charges, promoting complex formation. In cultures containing Mn2+ and As(III), As(III) started to be oxidized to As(V) after manganese oxide formation was mostly completed. In suspensions of the biogenic manganese oxides with dissolved Mn2+, As(III) oxidation rates decreased with increasing dissolved Mn2+. These results indicate that biogenic manganese oxide with a high proportion of bound Mn2+ oxidizes As(III) less effectively than with a low proportion of bound Mn2+. Coexisting Zn2+, Ni2+, and Co2+ also showed similar effects to different extents. The present study demonstrates characteristic features of oxidation and adsorption of As by biogenic manganese oxides and suggests possibilities of developing a microbial treatment system for water contaminated with As that is suited to the actual situation of contamination.
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Affiliation(s)
- Yukinori Tani
- Institute for Environmental Sciences, University of Shizuoka, 52-1 Yada, Shizuoka 422-8526, Japan.
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97
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Donachie SP, Hou S, Lee KS, Riley CW, Pikina A, Belisle C, Kempe S, Gregory TS, Bossuyt A, Boerema J, Liu J, Freitas TA, Malahoff A, Alam M. The Hawaiian Archipelago: a microbial diversity hotspot. MICROBIAL ECOLOGY 2004; 48:509-520. [PMID: 15696384 DOI: 10.1007/s00248-004-0217-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2003] [Accepted: 04/01/2004] [Indexed: 05/24/2023]
Abstract
The Hawaiian Archipelago is a "biodiversity hotspot" where significant endemism among eukaryotes has evolved through geographic isolation and local topography. To address the absence of corresponding region-wide data on Hawaii's microbiota, we compiled the first 16S SSU rDNA clone libraries and cultivated bacteria from five Hawaiian lakes, an anchialine pool, and the Lō'ihi submarine volcano. These sites offer diverse niches over approximately 5000 m elevation and approximately 1150 nautical miles. Each site hosted a distinct prokaryotic community dominated by Bacteria. Cloned sequences fell into 158 groups from 18 Bacteria phyla, while seven were unassigned and two belonged in the Euryarchaeota. Only seven operational taxonomic units (each OTU comprised sequences that shared > or =97% sequence identity) occurred in more than one site. Pure bacterial cultures from all sites fell into 155 groups (each group comprised pure cultures that shared > or =97% 16S SSU rDNA sequence identity) from 10 Bacteria phyla; 15 Proteobacteria and Firmicutes were cultivated from more than one site. One hundred OTUs (60%) and 52 (33.3%) cultures shared <97% 16S SSU rDNA sequence identity with published sequences. Community structure reflected habitat chemistry; most delta-Proteobacteria occurred in anoxic and sulfidic waters of one lake, while beta-Proteobacteria were cultivated exclusively from fresh or brackish waters. Novel sequences that affiliate with an Antarctic-specific clade of Deinococci, and Candidate Divisions TM7 and BRC1, extend the geographic ranges of these phyla. Globally and locally remote, as well as physically and chemically diverse, Hawaiian aquatic habitats provide unique niches for the evolution of novel communities and microorganisms.
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Affiliation(s)
- S P Donachie
- Department of Microbiology, University of Hawai, 2538 The Mall, Snyder Hall #111, Honolulu, HI 96822, USA
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98
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Molecular sequence analysis of prokaryotic diversity in the middle and outer sections of the Portuguese estuary Ria de Aveiro. FEMS Microbiol Ecol 2004; 49:269-79. [DOI: 10.1016/j.femsec.2004.04.003] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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99
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Quintanar L, Gebhard M, Wang TP, Kosman DJ, Solomon EI. Ferrous Binding to the Multicopper OxidasesSaccharomyces cerevisiaeFet3p and Human Ceruloplasmin: Contributions to Ferroxidase Activity. J Am Chem Soc 2004; 126:6579-89. [PMID: 15161286 DOI: 10.1021/ja049220t] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The multicopper oxidases are a family of enzymes that couple the reduction of O(2) to H(2)O with the oxidation of a range of substrates. Saccharomyces cerevisiae Fet3p and human ceruloplasmin (hCp) are members of this family that exhibit ferroxidase activity. Their high specificity for Fe(II) has been attributed to the existence of a binding site for iron. In this study, mutations at the E185 and Y354 residues, which are putative ligands for iron in Fet3p, have been generated and characterized. The effects of these mutations on the electronic structure of the T1 Cu site have been assessed, and the reactivities of this site toward 1,4-hydroquinone (a weak binding substrate) and Fe(II) have been evaluated and interpreted in terms of the semiclassical Marcus theory for electron transfer. The electronic and geometric structure of the Fe(II) substrate bound to Fet3p and hCp has been studied for the first time, using variable-temperature variable field magnetic circular dichroism (VTVH MCD) spectroscopy. The iron binding sites in Fet3p and hCp appear to be very similar in nature, and their contributions to the ferroxidase activity of these proteins have been analyzed. It is found that these iron binding sites play a major role in tuning the reduction potential of iron to provide a large driving force for the ferroxidase reaction, while still supporting the delivery of the Fe(III) product to the acceptor protein. Finally, the analysis of possible electron-transfer (ET) pathways from the protein-bound Fe(II) to the T1 Cu site indicates that the E185 residue not only plays a role in iron binding, but also provides the dominant ET pathway to the T1 Cu site.
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Affiliation(s)
- Liliana Quintanar
- Department of Chemistry, Stanford University, Stanford, California 94305-5080, USA
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100
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Larrondo LF, Salas L, Melo F, Vicuña R, Cullen D. A novel extracellular multicopper oxidase from Phanerochaete chrysosporium with ferroxidase activity. Appl Environ Microbiol 2004; 69:6257-63. [PMID: 14532088 PMCID: PMC201228 DOI: 10.1128/aem.69.10.6257-6263.2003] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Lignin degradation by the white rot basidiomycete Phanerochaete chrysosporium involves various extracellular oxidative enzymes, including lignin peroxidase, manganese peroxidase, and a peroxide-generating enzyme, glyoxal oxidase. Recent studies have suggested that laccases also may be produced by this fungus, but these conclusions have been controversial. We identified four sequences related to laccases and ferroxidases (Fet3) in a search of the publicly available P. chrysosporium database. One gene, designated mco1, has a typical eukaryotic secretion signal and is transcribed in defined media and in colonized wood. Structural analysis and multiple alignments identified residues common to laccase and Fet3 sequences. A recombinant MCO1 (rMCO1) protein expressed in Aspergillus nidulans had a molecular mass of 78 kDa, as determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, and the copper I-type center was confirmed by the UV-visible spectrum. rMCO1 oxidized various compounds, including 2,2'-azino(bis-3-ethylbenzthiazoline-6-sulfonate) (ABTS) and aromatic amines, although phenolic compounds were poor substrates. The best substrate was Fe2+, with a Km close to 2 micro M. Collectively, these results suggest that the P. chrysosporium genome does not encode a typical laccase but rather encodes a unique extracellular multicopper oxidase with strong ferroxidase activity.
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Affiliation(s)
- Luis F Larrondo
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
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