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Hemkemeyer M, Schwalb SA, Heinze S, Joergensen RG, Wichern F. Functions of elements in soil microorganisms. Microbiol Res 2021; 252:126832. [PMID: 34508963 DOI: 10.1016/j.micres.2021.126832] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 07/23/2021] [Accepted: 07/26/2021] [Indexed: 12/15/2022]
Abstract
The soil microbial community fulfils various functions, such as nutrient cycling and carbon (C) sequestration, therefore contributing to maintenance of soil fertility and mitigation of global warming. In this context, a major focus of research has been on C, nitrogen (N) and phosphorus (P) cycling. However, from aquatic and other environments, it is well known that other elements beyond C, N, and P are essential for microbial functioning. Nonetheless, for soil microorganisms this knowledge has not yet been synthesised. To gain a better mechanistic understanding of microbial processes in soil systems, we aimed at summarising the current knowledge on the function of a range of essential or beneficial elements, which may affect the efficiency of microbial processes in soil. This knowledge is discussed in the context of microbial driven nutrient and C cycling. Our findings may support future investigations and data evaluation, where other elements than C, N, and P affect microbial processes.
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Affiliation(s)
- Michael Hemkemeyer
- Department of Soil Science and Plant Nutrition, Institute of Biogenic Resources in Sustainable Food Systems - From Farm to Function, Rhine-Waal University of Applied Sciences, Marie-Curie-Str. 1, 47533 Kleve, Germany.
| | - Sanja A Schwalb
- Department of Soil Science and Plant Nutrition, Institute of Biogenic Resources in Sustainable Food Systems - From Farm to Function, Rhine-Waal University of Applied Sciences, Marie-Curie-Str. 1, 47533 Kleve, Germany
| | - Stefanie Heinze
- Department of Soil Science & Soil Ecology, Ruhr-University Bochum, Universitätsstr. 150, 44801 Bochum, Germany
| | - Rainer Georg Joergensen
- Department of Soil Biology and Plant Nutrition, University of Kassel, Nordbahnhofstr. 1a, 37213 Witzenhausen, Germany
| | - Florian Wichern
- Department of Soil Science and Plant Nutrition, Institute of Biogenic Resources in Sustainable Food Systems - From Farm to Function, Rhine-Waal University of Applied Sciences, Marie-Curie-Str. 1, 47533 Kleve, Germany
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Zhang M, Huang F, Wang G, Liu X, Wen J, Zhang X, Huang Y, Xia Y. Geographic distribution of cadmium and its interaction with the microbial community in the Longjiang River: risk evaluation after a shocking pollution accident. Sci Rep 2017; 7:227. [PMID: 28331217 PMCID: PMC5427973 DOI: 10.1038/s41598-017-00280-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 02/17/2017] [Indexed: 12/14/2022] Open
Abstract
A shocking Longjiang River cadmium pollution accident occurred in 2012, the effects of which on microbial communities remain unclear. Alkaline precipitation technology was applied for remediation, but concerns rose about the stability of this technology. To understand the geographic distribution of cadmium and its correlation with microbes, in this study, 39 water samples and 39 sludge samples from this river and 2 soil samples from the nearby farmland were collected for chemical and microbial analyses. The Cd concentrations of all water samples were lower than 0.005 mg/L and reached the quality standards for Chinese surface water. A ranking of sludge samples based on Cd contents showed sewage outfall > dosing sites > farmland, all of which were higher than the quality standard for soil. Alkaline precipitation technology was effective for Cd precipitation. Cd was unstable; it was constantly dissolving and being released from the sludge. The Cd content of each phase was mainly influenced by the total Cd content. Over 40,000 effective sequences were detected in each sample, and a total of 59,833 OTUs and 1,273 genera were found using Illumina MiSeq sequencing. Two phyla and 39 genera were notably positively correlated with the Cd distribution, while the cases of 10 phyla and 6 genera were the opposite.
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Affiliation(s)
- MingJiang Zhang
- National Engineering Laboratory of Biohydrometallurgy, General Research Institute for Nonferrous Metals, No. 2 Xinjiekouwai Street, Beijing, 100088, China
| | - FuKe Huang
- Institute of HeChi Scientific-Technical Information, No. 385 West Ring Road of HeChi City, GuangXi Zhuang Autonomous Region, 547000, China
| | - GuangYuan Wang
- National Engineering Laboratory of Biohydrometallurgy, General Research Institute for Nonferrous Metals, No. 2 Xinjiekouwai Street, Beijing, 100088, China
| | - XingYu Liu
- National Engineering Laboratory of Biohydrometallurgy, General Research Institute for Nonferrous Metals, No. 2 Xinjiekouwai Street, Beijing, 100088, China.
| | - JianKang Wen
- National Engineering Laboratory of Biohydrometallurgy, General Research Institute for Nonferrous Metals, No. 2 Xinjiekouwai Street, Beijing, 100088, China
| | - XiaoSheng Zhang
- Institute of HeChi Scientific-Technical Information, No. 385 West Ring Road of HeChi City, GuangXi Zhuang Autonomous Region, 547000, China
| | - YaoSi Huang
- Institute of HeChi Scientific-Technical Information, No. 385 West Ring Road of HeChi City, GuangXi Zhuang Autonomous Region, 547000, China
| | - Yu Xia
- National Engineering Laboratory of Biohydrometallurgy, General Research Institute for Nonferrous Metals, No. 2 Xinjiekouwai Street, Beijing, 100088, China
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Ray WC, Wolock SL, Callahan NW, Dong M, Li QQ, Liang C, Magliery TJ, Bartlett CW. Addressing the unmet need for visualizing conditional random fields in biological data. BMC Bioinformatics 2014; 15:202. [PMID: 25000815 PMCID: PMC4227292 DOI: 10.1186/1471-2105-15-202] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Accepted: 06/10/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The biological world is replete with phenomena that appear to be ideally modeled and analyzed by one archetypal statistical framework - the Graphical Probabilistic Model (GPM). The structure of GPMs is a uniquely good match for biological problems that range from aligning sequences to modeling the genome-to-phenome relationship. The fundamental questions that GPMs address involve making decisions based on a complex web of interacting factors. Unfortunately, while GPMs ideally fit many questions in biology, they are not an easy solution to apply. Building a GPM is not a simple task for an end user. Moreover, applying GPMs is also impeded by the insidious fact that the "complex web of interacting factors" inherent to a problem might be easy to define and also intractable to compute upon. DISCUSSION We propose that the visualization sciences can contribute to many domains of the bio-sciences, by developing tools to address archetypal representation and user interaction issues in GPMs, and in particular a variety of GPM called a Conditional Random Field(CRF). CRFs bring additional power, and additional complexity, because the CRF dependency network can be conditioned on the query data. CONCLUSIONS In this manuscript we examine the shared features of several biological problems that are amenable to modeling with CRFs, highlight the challenges that existing visualization and visual analytics paradigms induce for these data, and document an experimental solution called StickWRLD which, while leaving room for improvement, has been successfully applied in several biological research projects. Software and tutorials are available at http://www.stickwrld.org/.
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Affiliation(s)
- William C Ray
- Nationwide Children’s Hospital, 575 Children’s Crossroad, 43215 Columbus, OH, USA
- The Ohio State University, 100 W. 18th Ave, 43210 Columbus, OH, USA
| | - Samuel L Wolock
- Nationwide Children’s Hospital, 575 Children’s Crossroad, 43215 Columbus, OH, USA
| | | | - Min Dong
- Miami University, 501 E. High St., 45056 Oxford, OH, USA
| | - Q Quinn Li
- Miami University, 501 E. High St., 45056 Oxford, OH, USA
| | - Chun Liang
- Miami University, 501 E. High St., 45056 Oxford, OH, USA
| | | | - Christopher W Bartlett
- Nationwide Children’s Hospital, 575 Children’s Crossroad, 43215 Columbus, OH, USA
- The Ohio State University, 100 W. 18th Ave, 43210 Columbus, OH, USA
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Neuman NI, Winkler E, Peña O, Passeggi MCG, Rizzi AC, Brondino CD. Magnetic properties of weakly exchange-coupled high spin Co(II) ions in pseudooctahedral coordination evaluated by single crystal X-band EPR spectroscopy and magnetic measurements. Inorg Chem 2014; 53:2535-44. [PMID: 24528370 DOI: 10.1021/ic402797t] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
We report single-crystal X-band EPR and magnetic measurements of the coordination polymer catena-(trans-(μ2-fumarato)tetraaquacobalt(II)), 1, and the Co(II)-doped Zn(II) analogue, 2, in different Zn:Co ratios. 1 presents two magnetically inequivalent high spin S = 3/2 Co(II) ions per unit cell, named A and B, in a distorted octahedral environment coordinated to four water oxygen atoms and trans coordinated to two carboxylic oxygen atoms from the fumarate anions, in which the Co(II) ions are linked by hydrogen bonds and fumarate molecules. Magnetic susceptibility and magnetization measurements of 1 indicate weak antiferromagnetic exchange interactions between the S = 3/2 spins of the Co(II) ions in the crystal lattice. Oriented single crystal EPR experiments of 1 and 2 were used to evaluate the molecular g-tensor and the different exchange coupling constants between the Co(II) ions, assuming an effective spin S′= 1/2. Unexpectedly, the eigenvectors of the molecular g-tensor were not lying along any preferential bond direction, indicating that, in high spin Co(II) ions in roughly octahedral geometry with approximately axial EPR signals, the presence of molecular pseudo axes in the metal site does not determine preferential directions for the molecular g-tensor. The EPR experiment and magnetic measurements, together with a theoretical analysis relating the coupling constants obtained from both techniques, allowed us to evaluate selectively the exchange coupling constant associated with hydrogen bonds that connect magnetically inequivalent Co(II) ions (|JAB(1/2)| = 0.055(2) cm(–1)) and the exchange coupling constant associated with a fumarate bridge connecting equivalent Co(II) ions (|JAA(1/2)| ≈ 0.25 (1) cm(–1)), in good agreement with the average J(3/2) value determined from magnetic measurements.
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Affiliation(s)
- Nicolás I Neuman
- Departamento de Física, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral , S3000ZAA Santa Fe, Argentina
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Abhilash, Pandey B. Synthesis of zinc-based nanomaterials: a biological perspective. IET Nanobiotechnol 2012; 6:144-8. [DOI: 10.1049/iet-nbt.2011.0051] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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Armenta-Medina D, Pérez-Rueda E, Segovia L. Identification of functional motions in the adenylate kinase (ADK) protein family by computational hybrid approaches. Proteins 2011; 79:1662-71. [PMID: 21365689 DOI: 10.1002/prot.22995] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2010] [Revised: 12/03/2010] [Accepted: 12/07/2010] [Indexed: 02/02/2023]
Abstract
Based on integrative computational hybrid approaches that combined statistical coupling analysis (SCA), molecular dynamics (MD), and normal mode analysis (NMA), evolutionarily coupled residues involved in functionally relevant motion in the adenylate kinase protein family were identified. The hybrids identified four top-ranking site pairs that belong to a conserved hydrogen bond network that is involved in the enzyme's flexibility. A second group of top-ranking site pairs was identified in critical regions for functional dynamics, such as those related to enzymatic turnover. The high consistency of the results obtained by SCA with NMA (SCA.NMA) and by SCA.MD hybrid analyses suggests that suitable replacement of the matrix of cross-correlation analysis of atomic fluctuations (derived by using NMA) with those based on MD contributes to the identification of such sites by means of a fast computational calculation. The analysis presented here strongly supports the hypothesis that evolutionary forces, such as coevolution at the sequence level, have promoted functional dynamic properties of the adenylate kinase protein family. Finally, these hybrid approaches can be used to identify, at the residue level, protein motion coordination patterns not previously observed, such as in hinge regions.
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Affiliation(s)
- Dagoberto Armenta-Medina
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México.
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Crystal structure of the zinc-, cobalt-, and iron-containing adenylate kinase from Desulfovibrio gigas: a novel metal-containing adenylate kinase from Gram-negative bacteria. J Biol Inorg Chem 2010; 16:51-61. [PMID: 20821240 DOI: 10.1007/s00775-010-0700-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2010] [Accepted: 08/02/2010] [Indexed: 12/13/2022]
Abstract
Adenylate kinases (AK) from Gram-negative bacteria are generally devoid of metal ions in their LID domain. However, three metal ions, zinc, cobalt, and iron, have been found in AK from Gram-negative bacteria. Crystal structures of substrate-free AK from Desulfovibrio gigas with three different metal ions (Zn(2+), Zn-AK; Co(2+), Co-AK; and Fe(2+), Fe-AK) bound in its LID domain have been determined by X-ray crystallography to resolutions 1.8, 2.0, and 3.0 Å, respectively. The zinc and iron forms of the enzyme were crystallized in space group I222, whereas the cobalt-form crystals were C2. The presence of the metals was confirmed by calculation of anomalous difference maps and by X-ray fluorescence scans. The work presented here is the first report of a structure of a metal-containing AK from a Gram-negative bacterium. The native enzyme was crystallized, and only zinc was detected in the LID domain. Co-AK and Fe-AK were obtained by overexpressing the protein in Escherichia coli. Zn-AK and Fe-AK crystallized as monomers in the asymmetric unit, whereas Co-AK crystallized as a dimer. Nevertheless, all three crystal structures are very similar to each other, with the same LID domain topology, the only change being the presence of the different metal atoms. In the absence of any substrate, the LID domain of all holoforms of AK was present in a fully open conformational state. Normal mode analysis was performed to predict fluctuations of the LID domain along the catalytic pathway.
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Maganas D, Milikisyants S, Rijnbeek JMA, Sottini S, Levesanos N, Kyritsis P, Groenen EJJ. A Multifrequency High-Field Electron Paramagnetic Resonance Study of CoIIS4 Coordination. Inorg Chem 2009; 49:595-605. [DOI: 10.1021/ic901911h] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Dimitrios Maganas
- Inorganic Chemistry Laboratory, Department of Chemistry, National and Kapodistrian University of Athens, GR-15771 Athens, Greece
| | - Sergey Milikisyants
- Department of Molecular Physics, Huygens Laboratory, Leiden University, PO Box 9504, 2300 RA Leiden, The Netherlands
| | - Jorrit M. A. Rijnbeek
- Department of Molecular Physics, Huygens Laboratory, Leiden University, PO Box 9504, 2300 RA Leiden, The Netherlands
| | - Silvia Sottini
- Department of Molecular Physics, Huygens Laboratory, Leiden University, PO Box 9504, 2300 RA Leiden, The Netherlands
| | - Nikolaos Levesanos
- Inorganic Chemistry Laboratory, Department of Chemistry, National and Kapodistrian University of Athens, GR-15771 Athens, Greece
| | - Panayotis Kyritsis
- Inorganic Chemistry Laboratory, Department of Chemistry, National and Kapodistrian University of Athens, GR-15771 Athens, Greece
| | - Edgar J. J. Groenen
- Department of Molecular Physics, Huygens Laboratory, Leiden University, PO Box 9504, 2300 RA Leiden, The Netherlands
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Zinc-, cobalt- and iron-chelated forms of adenylate kinase from the Gram-negative bacterium Desulfovibrio gigas. Int J Biol Macromol 2009; 45:524-31. [DOI: 10.1016/j.ijbiomac.2009.09.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2009] [Accepted: 09/18/2009] [Indexed: 11/19/2022]
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Kladova AV, Gavel OY, Mukhopaadhyay A, Boer DR, Teixeira S, Shnyrov VL, Moura I, Moura JJG, Romão MJ, Trincão J, Bursakov SA. Cobalt-, zinc- and iron-bound forms of adenylate kinase (AK) from the sulfate-reducing bacterium Desulfovibrio gigas: purification, crystallization and preliminary X-ray diffraction analysis. Acta Crystallogr Sect F Struct Biol Cryst Commun 2009; 65:926-9. [PMID: 19724135 PMCID: PMC2795603 DOI: 10.1107/s1744309109029157] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2009] [Accepted: 07/22/2009] [Indexed: 11/11/2022]
Abstract
Adenylate kinase (AK; ATP:AMP phosphotransferase; EC 2.7.4.3) is involved in the reversible transfer of the terminal phosphate group from ATP to AMP. AKs contribute to the maintenance of a constant level of cellular adenine nucleotides, which is necessary for the energetic metabolism of the cell. Three metal ions, cobalt, zinc and iron(II), have been reported to be present in AKs from some Gram-negative bacteria. Native zinc-containing AK from Desulfovibrio gigas was purified to homogeneity and crystallized. The crystals diffracted to beyond 1.8 A resolution. Furthermore, cobalt- and iron-containing crystal forms of recombinant AK were also obtained and diffracted to 2.0 and 3.0 A resolution, respectively. Zn(2+)-AK and Fe(2+)-AK crystallized in space group I222 with similar unit-cell parameters, whereas Co(2+)-AK crystallized in space group C2; a monomer was present in the asymmetric unit for both the Zn(2+)-AK and Fe(2+)-AK forms and a dimer was present for the Co(2+)-AK form. The structures of the three metal-bound forms of AK will provide new insights into the role and selectivity of the metal in these enzymes.
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Affiliation(s)
- A. V. Kladova
- REQUIMTE, Departamento de Química, Centro de Química Fina e Biotecnologia, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - O. Yu. Gavel
- REQUIMTE, Departamento de Química, Centro de Química Fina e Biotecnologia, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
- Departamento de Bioquímica y Biología Molecular, Universidad de Salamanca, 37007 Salamanca, Spain
| | - A. Mukhopaadhyay
- REQUIMTE, Departamento de Química, Centro de Química Fina e Biotecnologia, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - D. R. Boer
- REQUIMTE, Departamento de Química, Centro de Química Fina e Biotecnologia, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - S. Teixeira
- REQUIMTE, Departamento de Química, Centro de Química Fina e Biotecnologia, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - V. L. Shnyrov
- Departamento de Bioquímica y Biología Molecular, Universidad de Salamanca, 37007 Salamanca, Spain
| | - I. Moura
- REQUIMTE, Departamento de Química, Centro de Química Fina e Biotecnologia, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - J. J. G. Moura
- REQUIMTE, Departamento de Química, Centro de Química Fina e Biotecnologia, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - M. J. Romão
- REQUIMTE, Departamento de Química, Centro de Química Fina e Biotecnologia, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - J. Trincão
- REQUIMTE, Departamento de Química, Centro de Química Fina e Biotecnologia, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - S. A. Bursakov
- REQUIMTE, Departamento de Química, Centro de Química Fina e Biotecnologia, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
- Departamento de Protección Ambiental, Estación Experimental del Zaidín, CSIC, C/Profesor Albareda 1, 18008 Granada, Spain
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Biochemistry, physiology and biotechnology of sulfate-reducing bacteria. ADVANCES IN APPLIED MICROBIOLOGY 2009; 68:41-98. [PMID: 19426853 DOI: 10.1016/s0065-2164(09)01202-7] [Citation(s) in RCA: 175] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Chemolithotrophic bacteria that use sulfate as terminal electron acceptor (sulfate-reducing bacteria) constitute a unique physiological group of microorganisms that couple anaerobic electron transport to ATP synthesis. These bacteria (220 species of 60 genera) can use a large variety of compounds as electron donors and to mediate electron flow they have a vast array of proteins with redox active metal groups. This chapter deals with the distribution in the environment and the major physiological and metabolic characteristics of sulfate-reducing bacteria (SRB). This chapter presents our current knowledge of soluble electron transfer proteins and transmembrane redox complexes that are playing an essential role in the dissimilatory sulfate reduction pathway of SRB of the genus Desulfovibrio. Environmentally important activities displayed by SRB are a consequence of the unique electron transport components or the production of high levels of H(2)S. The capability of SRB to utilize hydrocarbons in pure cultures and consortia has resulted in using these bacteria for bioremediation of BTEX (benzene, toluene, ethylbenzene and xylene) compounds in contaminated soils. Specific strains of SRB are capable of reducing 3-chlorobenzoate, chloroethenes, or nitroaromatic compounds and this has resulted in proposals to use SRB for bioremediation of environments containing trinitrotoluene and polychloroethenes. Since SRB have displayed dissimilatory reduction of U(VI) and Cr(VI), several biotechnology procedures have been proposed for using SRB in bioremediation of toxic metals. Additional non-specific metal reductase activity has resulted in using SRB for recovery of precious metals (e.g. platinum, palladium and gold) from waste streams. Since bacterially produced sulfide contributes to the souring of oil fields, corrosion of concrete, and discoloration of stonework is a serious problem, there is considerable interest in controlling the sulfidogenic activity of the SRB. The production of biosulfide by SRB has led to immobilization of toxic metals and reduction of textile dyes, although the process remains unresolved, SRB play a role in anaerobic methane oxidation which not only contributes to carbon cycle activities but also depletes an important industrial energy reserve.
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