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Li Z, Li Y, Cheng W. Determination of cinnamaldehyde, thymol and eugenol in essential oils by LC-MS/MS and antibacterial activity of them against bacteria. Sci Rep 2024; 14:12424. [PMID: 38816435 PMCID: PMC11139912 DOI: 10.1038/s41598-024-63114-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 05/24/2024] [Indexed: 06/01/2024] Open
Abstract
Plant essential oils contain many secondary metabolites, some of which can effectively inhibit the growth of pathogenic microorganisms, so it is a very promising antibacterial agent. In this study, a qualitative and quantitative method based on high performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) was developed for the simultaneous determination of three bioactive substances, cinnamaldehyde (CNM), thymol (THY), and eugenol (EUG), in the essential oils of plants. Necessary tests for linearity, limit of quantification, recovery, carryover contamination and precision of the method were carried out. Then, the antibacterial activity of 3 bioactive compounds against Escherichia coli (E. coli) and Staphylococcus aureus (S. aureus) was evaluated by minimal inhibitory concentration and the synergistic antimicrobial effect. The results indicated that CNM, THY and EUG had good antibacterial activity. According to the results of fractional inhibitory concentration index (FICI), it is considered that CNM + THY and CNM + THY + EUG has obvious synergistic inhibitory effect on E. coli, and CNM + THY and CNM + EUG has obvious synergistic inhibitory effect on S. aureus. Finally, we analyzed the effect of the bioactive compounds on trace elements in bacteria and found significant changes in magnesium, calcium, copper and iron.
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Affiliation(s)
- Zhi Li
- Tianjin Guoke Medical Technology Development Co., LTD, Tianjin, 300399, China
| | - Yan Li
- Tianjin Guoke Medical Technology Development Co., LTD, Tianjin, 300399, China
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China
| | - Wenbo Cheng
- Tianjin Guoke Medical Technology Development Co., LTD, Tianjin, 300399, China.
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China.
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2
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Metalloenzyme signatures in authigenic carbonates from the Chukchi Borderlands in the western Arctic Ocean. Sci Rep 2022; 12:16597. [PMID: 36198754 PMCID: PMC9534989 DOI: 10.1038/s41598-022-21184-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 09/23/2022] [Indexed: 11/08/2022] Open
Abstract
Migration of methane-rich fluids at submarine cold seeps drives intense microbial activity and precipitation of authigenic carbonates. In this study, we analyzed microbially derived authigenic carbonate samples recently recovered from active gas hydrate mounds on the southwestern slope of the Chukchi Borderlands (CB), western Arctic Ocean. Our main aim was to characterize the distribution patterns of trace elements in carbonate-hosted lipid fractions to assess metalloenzyme requirements of microbes involved in anaerobic oxidation of methane (AOM). We measured stable isotopes, trace elements, lipid biomarkers, and genomic DNA, and results indicate the dominance of AOM-related lipid biomarkers in studied carbonate samples, as well as a predominant occurrence of the anaerobic methanotrophic archaea (ANME)-1. We also report evidence for significant preferential enrichments of various trace elements (Li, Ni, Co, Cu, Zn, and Mo) in the total lipid fractions of CB carbonates, relative to elemental compositions determined for corresponding carbonate fractions, which differ from those previously reported for other seep sites. We hypothesize that trace element enrichments in carbonate-hosted lipid fractions could vary depending on the type of AOM microbial assemblage. Additional work is required to further investigate the mechanisms of lipid-bound trace elements in cold seep carbonates as potential metalloenzymes in AOM.
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3
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Tripathi AK, Saxena P, Thakur P, Rauniyar S, Samanta D, Gopalakrishnan V, Singh RN, Sani RK. Transcriptomics and Functional Analysis of Copper Stress Response in the Sulfate-Reducing Bacterium Desulfovibrio alaskensis G20. Int J Mol Sci 2022; 23:ijms23031396. [PMID: 35163324 PMCID: PMC8836040 DOI: 10.3390/ijms23031396] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Revised: 01/20/2022] [Accepted: 01/24/2022] [Indexed: 01/27/2023] Open
Abstract
Copper (Cu) is an essential micronutrient required as a co-factor in the catalytic center of many enzymes. However, excess Cu can generate pleiotropic effects in the microbial cell. In addition, leaching of Cu from pipelines results in elevated Cu concentration in the environment, which is of public health concern. Sulfate-reducing bacteria (SRB) have been demonstrated to grow in toxic levels of Cu. However, reports on Cu toxicity towards SRB have primarily focused on the degree of toxicity and subsequent elimination. Here, Cu(II) stress-related effects on a model SRB, Desulfovibrio alaskensis G20, is reported. Cu(II) stress effects were assessed as alterations in the transcriptome through RNA-Seq at varying Cu(II) concentrations (5 µM and 15 µM). In the pairwise comparison of control vs. 5 µM Cu(II), 61.43% of genes were downregulated, and 38.57% were upregulated. In control vs. 15 µM Cu(II), 49.51% of genes were downregulated, and 50.5% were upregulated. The results indicated that the expression of inorganic ion transporters and translation machinery was massively modulated. Moreover, changes in the expression of critical biological processes such as DNA transcription and signal transduction were observed at high Cu(II) concentrations. These results will help us better understand the Cu(II) stress-response mechanism and provide avenues for future research.
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Affiliation(s)
- Abhilash Kumar Tripathi
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA; (A.K.T.); (P.S.); (P.T.); (S.R.); (D.S.); (V.G.); (R.N.S.)
- 2-Dimensional Materials for Biofilm Engineering, Science and Technology, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA
| | - Priya Saxena
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA; (A.K.T.); (P.S.); (P.T.); (S.R.); (D.S.); (V.G.); (R.N.S.)
- Data Driven Material Discovery Center for Bioengineering Innovation, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA
| | - Payal Thakur
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA; (A.K.T.); (P.S.); (P.T.); (S.R.); (D.S.); (V.G.); (R.N.S.)
- Data Driven Material Discovery Center for Bioengineering Innovation, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA
| | - Shailabh Rauniyar
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA; (A.K.T.); (P.S.); (P.T.); (S.R.); (D.S.); (V.G.); (R.N.S.)
- 2-Dimensional Materials for Biofilm Engineering, Science and Technology, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA
| | - Dipayan Samanta
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA; (A.K.T.); (P.S.); (P.T.); (S.R.); (D.S.); (V.G.); (R.N.S.)
- BuG ReMeDEE Consortium, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA
| | - Vinoj Gopalakrishnan
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA; (A.K.T.); (P.S.); (P.T.); (S.R.); (D.S.); (V.G.); (R.N.S.)
- Data Driven Material Discovery Center for Bioengineering Innovation, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA
| | - Ram Nageena Singh
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA; (A.K.T.); (P.S.); (P.T.); (S.R.); (D.S.); (V.G.); (R.N.S.)
- 2-Dimensional Materials for Biofilm Engineering, Science and Technology, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA
| | - Rajesh Kumar Sani
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA; (A.K.T.); (P.S.); (P.T.); (S.R.); (D.S.); (V.G.); (R.N.S.)
- 2-Dimensional Materials for Biofilm Engineering, Science and Technology, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA
- Data Driven Material Discovery Center for Bioengineering Innovation, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA
- BuG ReMeDEE Consortium, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA
- Composite and Nanocomposite Advanced Manufacturing Centre—Biomaterials, Rapid City, SD 57701, USA
- Correspondence:
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Ahnert M, Schalk T, Brückner H, Effenberger J, Kuehn V, Krebs P. Organic matter parameters in WWTP - a critical review and recommendations for application in activated sludge modelling. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2021; 84:2093-2112. [PMID: 34810300 DOI: 10.2166/wst.2021.419] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
This paper includes a comprehensive literature review of sludge composition data from wastewater treatment plants. 722 data sets from 249 sources were used to establish typical ratios between COD and solids-based parameters and to verify rule-of-thumb values, respectively. Confirmation of these typical ratios can also be accomplished by using biochemical composition data. It is shown that a correlation between data from proteins, lipids and carbohydrates analysis can be related to COD/VSS ratios. Finally, using the findings from the literature review, the organic and inorganic conversion factors of COD fractions in activated sludge models are adjusted to solids-based parameters. It was shown that with the adjustments of the factors and a partition of the particulate inert fraction into a fraction assigned to the influent and a fraction assigned to the endogenous products, a better agreement with the ratios of COD/VSS in the individual sludge streams can be established.
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Affiliation(s)
- Markus Ahnert
- Technische Universität Dresden, Institute of Urban and Industrial Water Management, 01062 Dresden, Germany E-mail:
| | - Thomas Schalk
- Technische Universität Dresden, Institute of Urban and Industrial Water Management, 01062 Dresden, Germany E-mail:
| | - Heike Brückner
- Technische Universität Dresden, Institute of Urban and Industrial Water Management, 01062 Dresden, Germany E-mail:
| | | | - Volker Kuehn
- Stadtentwässerung Dresden GmbH, Scharfenberger Str. 152, 01139 Dresden, Germany
| | - Peter Krebs
- Technische Universität Dresden, Institute of Urban and Industrial Water Management, 01062 Dresden, Germany E-mail:
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von Rosen T, Keller LM, Weber-Ban E. Survival in Hostile Conditions: Pupylation and the Proteasome in Actinobacterial Stress Response Pathways. Front Mol Biosci 2021; 8:685757. [PMID: 34179091 PMCID: PMC8223512 DOI: 10.3389/fmolb.2021.685757] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 05/04/2021] [Indexed: 12/31/2022] Open
Abstract
Bacteria employ a multitude of strategies to cope with the challenges they face in their natural surroundings, be it as pathogens, commensals or free-living species in rapidly changing environments like soil. Mycobacteria and other Actinobacteria acquired proteasomal genes and evolved a post-translational, ubiquitin-like modification pathway called pupylation to support their survival under rapidly changing conditions and under stress. The proteasomal 20S core particle (20S CP) interacts with ring-shaped activators like the hexameric ATPase Mpa that recruits pupylated substrates. The proteasomal subunits, Mpa and pupylation enzymes are encoded in the so-called Pup-proteasome system (PPS) gene locus. Genes in this locus become vital for bacteria to survive during periods of stress. In the successful human pathogen Mycobacterium tuberculosis, the 20S CP is essential for survival in host macrophages. Other members of the PPS and proteasomal interactors are crucial for cellular homeostasis, for example during the DNA damage response, iron and copper regulation, and heat shock. The multiple pathways that the proteasome is involved in during different stress responses suggest that the PPS plays a vital role in bacterial protein quality control and adaptation to diverse challenging environments.
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Affiliation(s)
- Tatjana von Rosen
- Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Lena Ml Keller
- Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Eilika Weber-Ban
- Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
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6
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Genetic Basis of Chromate Adaptation and the Role of the Pre-existing Genetic Divergence during an Experimental Evolution Study with Desulfovibrio vulgaris Populations. mSystems 2021; 6:e0049321. [PMID: 34061571 PMCID: PMC8579811 DOI: 10.1128/msystems.00493-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Hexavalent chromium [Cr(VI)] is a common environmental pollutant. However, little is known about the genetic basis of microbial evolution under Cr(VI) stress and the influence of the prior evolution histories on the subsequent evolution under Cr(VI) stress. In this study, Desulfovibrio vulgaris Hildenborough (DvH), a model sulfate-reducing bacterium, was experimentally evolved for 600 generations. By evolving the replicate populations of three genetically diverse DvH clones, including ancestor (AN, without prior experimental evolution history), non-stress-evolved EC3-10, and salt stress-evolved ES9-11, the contributions of adaptation, chance, and pre-existing genetic divergence to the evolution under Cr(VI) stress were able to be dissected. Significantly decreased lag phases under Cr(VI) stress were observed in most evolved populations, while increased Cr(VI) reduction rates were primarily observed in populations evolved from EC3-10 and ES9-11. The pre-existing genetic divergence in the starting clones showed strong influences on the changes in lag phases, growth rates, and Cr(VI) reduction rates. Additionally, the genomic mutation spectra in populations evolved from different starting clones were significantly different. A total of 14 newly mutated genes obtained mutations in at least two evolved populations, suggesting their importance in Cr(VI) adaptation. An in-frame deletion mutation of one of these genes, the chromate transporter gene DVU0426, demonstrated that it played an important role in Cr(VI) tolerance. Overall, our study identified potential key functional genes for Cr(VI) tolerance and demonstrated the important role of pre-existing genetic divergence in evolution under Cr(VI) stress conditions. IMPORTANCE Chromium is one of the most common heavy metal pollutants of soil and groundwater. The potential of Desulfovibrio vulgaris Hildenborough in heavy metal bioremediation such as Cr(VI) reduction was reported previously; however, experimental evidence of key functional genes involved in Cr(VI) resistance are largely unknown. Given the genetic divergence of microbial populations in nature, knowledge on how this divergence affects the microbial adaptation to a new environment such as Cr(VI) stress is very limited. Taking advantage of our previous study, three groups of genetically diverse D. vulgaris Hildenborough populations with or without prior experimental evolution histories were propagated under Cr(VI) stress for 600 generations. Whole-population genome resequencing of the evolved populations revealed the genomic changes underlying the improved Cr(VI) tolerance. The strong influence of the pre-existing genetic divergence in the starting clones on evolution under Cr(VI) stress conditions was demonstrated at both phenotypic and genetic levels.
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7
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Jaafar NR, Khoiri NM, Ismail NF, Mahmood NAN, Abdul Murad AM, Abu Bakar FD, Mat Yajit NL, Illias RM. Functional characterisation and product specificity of Endo-β-1,3-glucanase from alkalophilic bacterium, Bacillus lehensis G1. Enzyme Microb Technol 2020; 140:109625. [DOI: 10.1016/j.enzmictec.2020.109625] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 05/30/2020] [Accepted: 06/11/2020] [Indexed: 12/28/2022]
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8
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Song Y, Adediran GA, Jiang T, Hayama S, Björn E, Skyllberg U. Toward an Internally Consistent Model for Hg(II) Chemical Speciation Calculations in Bacterium-Natural Organic Matter-Low Molecular Mass Thiol Systems. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:8094-8103. [PMID: 32491838 PMCID: PMC7467648 DOI: 10.1021/acs.est.0c01751] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
To advance the scientific understanding of bacteria-driven mercury (Hg) transformation processes in natural environments, thermodynamics and kinetics of divalent mercury Hg(II) chemical speciation need to be understood. Based on Hg LIII-edge extended X-ray absorption fine structure (EXAFS) spectroscopic information, combined with competitive ligand exchange (CLE) experiments, we determined Hg(II) structures and thermodynamic constants for Hg(II) complexes formed with thiol functional groups in bacterial cell membranes of two extensively studied Hg(II) methylating bacteria: Geobacter sulfurreducens PCA and Desulfovibrio desulfuricans ND132. The Hg EXAFS data suggest that 5% of the total number of membranethiol functionalities (Mem-RStot = 380 ± 50 μmol g-1 C) are situated closely enough to be involved in a 2-coordinated Hg(Mem-RS)2 structure in Geobacter. The remaining 95% of Mem-RSH is involved in mixed-ligation Hg(II)-complexes, combining either with low molecular mass (LMM) thiols like Cys, Hg(Cys)(Mem-RS), or with neighboring O/N membrane functionalities, Hg(Mem-RSRO). We report log K values for the formation of the structures Hg(Mem-RS)2, Hg(Cys)(Mem-RS), and Hg(Mem-RSRO) to be 39.1 ± 0.2, 38.1 ± 0.1, and 25.6 ± 0.1, respectively, for Geobacter and 39.2 ± 0.2, 38.2 ± 0.1, and 25.7 ± 0.1, respectively, for ND132. Combined with results obtained from previous studies using the same methodology to determine chemical speciation of Hg(II) in the presence of natural organic matter (NOM; Suwannee River DOM) and 15 LMM thiols, an internally consistent thermodynamic data set is created, which we recommend to be used in studies of Hg transformation processes in bacterium-NOM-LMM thiol systems.
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Affiliation(s)
- Yu Song
- Department
of Forest Ecology and Management, Swedish
University of Agricultural Science, SE-901 83 Umeå, Sweden
| | | | - Tao Jiang
- Department
of Forest Ecology and Management, Swedish
University of Agricultural Science, SE-901 83 Umeå, Sweden
| | - Shusaku Hayama
- Diamond
Light Source, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - Erik Björn
- Department
of Chemistry, Umeå University, SE-901 87 Umeå, Sweden
| | - Ulf Skyllberg
- Department
of Forest Ecology and Management, Swedish
University of Agricultural Science, SE-901 83 Umeå, Sweden
- . Phone: +46 (0)90-786 84 60
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9
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Reed KB, Alper HS. Expanding beyond canonical metabolism: Interfacing alternative elements, synthetic biology, and metabolic engineering. Synth Syst Biotechnol 2018; 3:20-33. [PMID: 29911196 PMCID: PMC5884228 DOI: 10.1016/j.synbio.2017.12.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 11/08/2017] [Accepted: 12/09/2017] [Indexed: 12/15/2022] Open
Abstract
Metabolic engineering offers an exquisite capacity to produce new molecules in a renewable manner. However, most industrial applications have focused on only a small subset of elements from the periodic table, centered around carbon biochemistry. This review aims to illustrate the expanse of chemical elements that can currently (and potentially) be integrated into useful products using cellular systems. Specifically, we describe recent advances in expanding the cellular scope to include the halogens, selenium and the metalloids, and a variety of metal incorporations. These examples range from small molecules, heteroatom-linked uncommon elements, and natural products to biomining and nanotechnology applications. Collectively, this review covers the promise of an expanded range of elemental incorporations and the future impacts it may have on biotechnology.
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Affiliation(s)
- Kevin B. Reed
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200E Dean Keeton St. Stop C0400, Austin, TX 78712, USA
| | - Hal S. Alper
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200E Dean Keeton St. Stop C0400, Austin, TX 78712, USA
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, 2500 Speedway Avenue, Austin, TX 78712, USA
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10
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Bao P, Li GX, Sun GX, Xu YY, Meharg AA, Zhu YG. The role of sulfate-reducing prokaryotes in the coupling of element biogeochemical cycling. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 613-614:398-408. [PMID: 28918271 DOI: 10.1016/j.scitotenv.2017.09.062] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 09/07/2017] [Accepted: 09/07/2017] [Indexed: 06/07/2023]
Abstract
Sulfate-reducing prokaryotes (SRP) represent a diverse group of heterotrophic and autotrophic microorganisms that are ubiquitous in anoxic habitats. In addition to their important role in both sulfur and carbon cycles, SRP are important biotic and abiotic regulators of a variety of sulfur-driven coupled biogeochemical cycling of elements, including: oxygen, nitrogen, chlorine, bromine, iodine and metal(loid)s. SRP gain energy form most of the coupling of element transformation. Once sulfate-reducing conditions are established, sulfide precipitation becomes the predominant abiotic mechanism of metal(loid)s transformation, followed by co-precipitation between metal(loid)s. Anthropogenic contamination, since the industrial revolution, has dramatically disturbed sulfur-driven biogeochemical cycling; making sulfur coupled elements transformation complicated and unpredictable. We hypothesise that sulfur might be detoxication agent for the organic and inorganic toxic compounds, through the metabolic activity of SRP. This review synthesizes the recent advances in the role of SRP in coupled biogeochemical cycling of diverse elements.
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Affiliation(s)
- Peng Bao
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, PR China; Ningbo Urban Environment Observation and Station, Chinese Academy of Sciences, Ningbo 315800, PR China
| | - Guo-Xiang Li
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, PR China; Ningbo Urban Environment Observation and Station, Chinese Academy of Sciences, Ningbo 315800, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Guo-Xin Sun
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100086, PR China
| | - Yao-Yang Xu
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, PR China; Ningbo Urban Environment Observation and Station, Chinese Academy of Sciences, Ningbo 315800, PR China
| | - Andrew A Meharg
- Institute of Global Food Security, Queen's University Belfast, David Keir Building, Stranmillis Road, Belfast BT9 5AG, United Kingdom
| | - Yong-Guan Zhu
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, PR China; State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100086, PR China.
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11
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Kalathil S, Pant D. Nanotechnology to rescue bacterial bidirectional extracellular electron transfer in bioelectrochemical systems. RSC Adv 2016. [DOI: 10.1039/c6ra04734c] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Advanced nanostructured electrode materials largely improve the bacterial bidirectional extracellular electron transfer in bioelectrochemical systems.
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Affiliation(s)
- Shafeer Kalathil
- Division of Biological and Environmental Science & Engineering
- King Abdullah University of Science and Technology
- Thuwal 23955-6900
- Saudi Arabia
| | - Deepak Pant
- Separation and Conversion Technology
- VITO – Flemish Institute for Technological Research
- 2400 Mol
- Belgium
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12
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A Post-Genomic View of the Ecophysiology, Catabolism and Biotechnological Relevance of Sulphate-Reducing Prokaryotes. Adv Microb Physiol 2015. [PMID: 26210106 DOI: 10.1016/bs.ampbs.2015.05.002] [Citation(s) in RCA: 173] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Dissimilatory sulphate reduction is the unifying and defining trait of sulphate-reducing prokaryotes (SRP). In their predominant habitats, sulphate-rich marine sediments, SRP have long been recognized to be major players in the carbon and sulphur cycles. Other, more recently appreciated, ecophysiological roles include activity in the deep biosphere, symbiotic relations, syntrophic associations, human microbiome/health and long-distance electron transfer. SRP include a high diversity of organisms, with large nutritional versatility and broad metabolic capacities, including anaerobic degradation of aromatic compounds and hydrocarbons. Elucidation of novel catabolic capacities as well as progress in the understanding of metabolic and regulatory networks, energy metabolism, evolutionary processes and adaptation to changing environmental conditions has greatly benefited from genomics, functional OMICS approaches and advances in genetic accessibility and biochemical studies. Important biotechnological roles of SRP range from (i) wastewater and off gas treatment, (ii) bioremediation of metals and hydrocarbons and (iii) bioelectrochemistry, to undesired impacts such as (iv) souring in oil reservoirs and other environments, and (v) corrosion of iron and concrete. Here we review recent advances in our understanding of SRPs focusing mainly on works published after 2000. The wealth of publications in this period, covering many diverse areas, is a testimony to the large environmental, biogeochemical and technological relevance of these organisms and how much the field has progressed in these years, although many important questions and applications remain to be explored.
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Beese-Vasbender PF, Nayak S, Erbe A, Stratmann M, Mayrhofer KJ. Electrochemical characterization of direct electron uptake in electrical microbially influenced corrosion of iron by the lithoautotrophic SRB Desulfopila corrodens strain IS4. Electrochim Acta 2015. [DOI: 10.1016/j.electacta.2015.03.184] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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14
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Liu XW, Li WW, Yu HQ. Cathodic catalysts in bioelectrochemical systems for energy recovery from wastewater. Chem Soc Rev 2014; 43:7718-45. [DOI: 10.1039/c3cs60130g] [Citation(s) in RCA: 183] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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15
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Aklujkar M, Coppi MV, Leang C, Kim BC, Chavan MA, Perpetua LA, Giloteaux L, Liu A, Holmes DE. Proteins involved in electron transfer to Fe(III) and Mn(IV) oxides by Geobacter sulfurreducens and Geobacter uraniireducens. MICROBIOLOGY-SGM 2013; 159:515-535. [PMID: 23306674 DOI: 10.1099/mic.0.064089-0] [Citation(s) in RCA: 117] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Whole-genome microarray analysis of Geobacter sulfurreducens grown on insoluble Fe(III) oxide or Mn(IV) oxide versus soluble Fe(III) citrate revealed significantly different expression patterns. The most upregulated genes, omcS and omcT, encode cell-surface c-type cytochromes, OmcS being required for Fe(III) and Mn(IV) oxide reduction. Other electron transport genes upregulated on both metal oxides included genes encoding putative menaquinol : ferricytochrome c oxidoreductase complexes Cbc4 and Cbc5, periplasmic c-type cytochromes Dhc2 and PccF, outer membrane c-type cytochromes OmcC, OmcG and OmcV, multicopper oxidase OmpB, the structural components of electrically conductive pili, PilA-N and PilA-C, and enzymes that detoxify reactive oxygen/nitrogen species. Genes upregulated on Fe(III) oxide encode putative menaquinol : ferricytochrome c oxidoreductase complexes Cbc3 and Cbc6, periplasmic c-type cytochromes, including PccG and PccJ, and outer membrane c-type cytochromes, including OmcA, OmcE, OmcH, OmcL, OmcN, OmcO and OmcP. Electron transport genes upregulated on Mn(IV) oxide encode periplasmic c-type cytochromes PccR, PgcA, PpcA and PpcD, outer membrane c-type cytochromes OmaB/OmaC, OmcB and OmcZ, multicopper oxidase OmpC and menaquinone-reducing enzymes. Genetic studies indicated that MacA, OmcB, OmcF, OmcG, OmcH, OmcI, OmcJ, OmcM, OmcV and PccH, the putative Cbc5 complex subunit CbcC and the putative Cbc3 complex subunit CbcV are important for reduction of Fe(III) oxide but not essential for Mn(IV) oxide reduction. Gene expression patterns for Geobacter uraniireducens were similar. These results demonstrate that the physiology of Fe(III)-reducing bacteria differs significantly during growth on different insoluble and soluble electron acceptors and emphasize the importance of c-type cytochromes for extracellular electron transfer in G. sulfurreducens.
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Affiliation(s)
- M Aklujkar
- Department of Microbiology, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - M V Coppi
- Department of Microbiology, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - C Leang
- Department of Microbiology, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - B C Kim
- Department of Microbiology, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - M A Chavan
- Department of Microbiology, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - L A Perpetua
- Department of Microbiology, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - L Giloteaux
- Department of Microbiology, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - A Liu
- Department of Mathematics and Statistics, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - D E Holmes
- Department of Physical and Biological Sciences, Western New England University, Springfield, MA 01119, USA
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16
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Wang D. Redox chemistry of molybdenum in natural waters and its involvement in biological evolution. Front Microbiol 2012; 3:427. [PMID: 23267355 PMCID: PMC3528336 DOI: 10.3389/fmicb.2012.00427] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2012] [Accepted: 12/03/2012] [Indexed: 11/13/2022] Open
Abstract
The transition element molybdenum (Mo) possesses diverse valances (+II to +VI), and is involved in forming cofactors in more than 60 enzymes in biology. Redox switching of the element in these enzymes catalyzes a series of metabolic reactions in both prokaryotes and eukaryotes, and the element therefore plays a fundamental role in the global carbon, nitrogen, and sulfur cycling. In the present oxygenated waters, oxidized Mo(VI) predominates thermodynamically, whilst reduced Mo species are mainly confined within specific niches including cytoplasm. Only recently has the reduced Mo(V) been separated from Mo(VI) in sulfidic mats and even in some reducing waters. Given the presence of reduced Mo(V) in contemporary anaerobic habitats, it seems that reduced Mo species were present in the ancient reducing ocean (probably under both ferruginous and sulfidic conditions), prompting the involvement of Mo in enzymes including nitrogenase and nitrate reductase. During the global transition to oxic conditions, reduced Mo species were constrained to specific anaerobic habitats, and efficient uptake systems of oxidized Mo(VI) became a selective advantage for current prokaryotic and eukaryotic cells. Some prokaryotes are still able to directly utilize reduced Mo if any exists in ambient environments. In total, this mini-review describes the redox chemistry and biogeochemistry of Mo over the Earth’s history.
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Affiliation(s)
- Deli Wang
- State Key Laboratory of Marine Environmental Science, Xiamen University Xiamen, China
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17
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Gonzalez-Gil G, Lopes SIC, Saikaly PE, Lens PNL. Leaching and accumulation of trace elements in sulfate reducing granular sludge under concomitant thermophilic and low pH conditions. BIORESOURCE TECHNOLOGY 2012; 126:238-246. [PMID: 23073114 DOI: 10.1016/j.biortech.2012.09.044] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2012] [Revised: 09/11/2012] [Accepted: 09/13/2012] [Indexed: 06/01/2023]
Abstract
The leaching and/or accumulation of trace elements in sulfate reducing granular sludge systems was investigated. Two thermophilic up-flow anaerobic sludge bed (UASB) reactors operated at pH 5 were fed with sucrose (4 gCOD l(reactor)(-1)d(-1)) and sulfate at different COD/SO(4)(2-) ratios. During the start-up of such acidogenic systems, an initial leaching of trace elements from the inoculum sludge occurred regardless of trace elements supplementation in the reactor influent. The granular sludge maintained the physical structure despite high Fe leaching. After start-up and nonetheless the acidic conditions, Co, Ni, Cu, Zn, Mo and Se were retained or accumulated by the sludge when added. Particularly, Ni and Co accumulated in the carbonates and exchangeable fractions ensuring potential bioavailability. Otherwise, the initial stock in the inoculum sludge sufficed to operate the process for nearly 1 year without supplementation of trace elements and no significant sludge wash-out occurred.
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Affiliation(s)
- G Gonzalez-Gil
- Pollution Prevention and Control Core, UNESCO-IHE, Westvest 7, 2611 AX Delft, The Netherlands
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18
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Giacomucci L, Toja F, Sanmartín P, Toniolo L, Prieto B, Villa F, Cappitelli F. Degradation of nitrocellulose-based paint by Desulfovibrio desulfuricans ATCC 13541. Biodegradation 2012; 23:705-16. [PMID: 22367465 DOI: 10.1007/s10532-012-9546-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2011] [Accepted: 02/15/2012] [Indexed: 11/24/2022]
Abstract
Nitrocellulose is one of the most commonly used compounds in ammunition and paint industries and its recalcitrance to degradation has a negative impact on human health and the environment. In this study the capability of Desulfovibrio desulfuricans ATCC 13541 to degrade nitrocellulose as binder in paint was assayed for the first time. Nitrocellulose-based paint degradation was followed by monitoring the variation in nitrate, nitrite and ammonium content in the culture medium using Ultraviolet-Visible spectroscopy. At the same time cell counts and ATP assay were performed to estimate bacterial density and activity in all samples. Infrared spectroscopy and colorimetric measurements of paint samples were performed to assess chemical and colour changes due to the microbial action. Microscope observations of nitrocellulose-based paint samples demonstrated the capability of the bacterium to adhere to the paint surface and change the paint adhesive characteristics. Finally, preliminary studies of nitrocellulose degradation pathway were conducted by assaying nitrate- and nitrite reductases activity in D. desulfuricans grown in presence or in absence of paint. We found that D. desulfuricans ATCC 13541 is able to transform nitrocellulose as paint binder and we hypothesised ammonification as degradation pathway. The results suggest that D. desulfuricans ATCC 13541 is a good candidate as a nitrocellulose-degrading bacterium.
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Affiliation(s)
- L Giacomucci
- Dipartimento di Scienze e Tecnologie Alimentari e Microbiologiche, Università degli Studi di Milano, Via Celoria 2, 20133 Milan, Italy
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19
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Glass JB, Orphan VJ. Trace metal requirements for microbial enzymes involved in the production and consumption of methane and nitrous oxide. Front Microbiol 2012; 3:61. [PMID: 22363333 PMCID: PMC3282944 DOI: 10.3389/fmicb.2012.00061] [Citation(s) in RCA: 158] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2011] [Accepted: 02/05/2012] [Indexed: 01/15/2023] Open
Abstract
Fluxes of greenhouse gases to the atmosphere are heavily influenced by microbiological activity. Microbial enzymes involved in the production and consumption of greenhouse gases often contain metal cofactors. While extensive research has examined the influence of Fe bioavailability on microbial CO(2) cycling, fewer studies have explored metal requirements for microbial production and consumption of the second- and third-most abundant greenhouse gases, methane (CH(4)), and nitrous oxide (N(2)O). Here we review the current state of biochemical, physiological, and environmental research on transition metal requirements for microbial CH(4) and N(2)O cycling. Methanogenic archaea require large amounts of Fe, Ni, and Co (and some Mo/W and Zn). Low bioavailability of Fe, Ni, and Co limits methanogenesis in pure and mixed cultures and environmental studies. Anaerobic methane oxidation by anaerobic methanotrophic archaea (ANME) likely occurs via reverse methanogenesis since ANME possess most of the enzymes in the methanogenic pathway. Aerobic CH(4) oxidation uses Cu or Fe for the first step depending on Cu availability, and additional Fe, Cu, and Mo for later steps. N(2)O production via classical anaerobic denitrification is primarily Fe-based, whereas aerobic pathways (nitrifier denitrification and archaeal ammonia oxidation) require Cu in addition to, or possibly in place of, Fe. Genes encoding the Cu-containing N(2)O reductase, the only known enzyme capable of microbial N(2)O conversion to N(2), have only been found in classical denitrifiers. Accumulation of N(2)O due to low Cu has been observed in pure cultures and a lake ecosystem, but not in marine systems. Future research is needed on metalloenzymes involved in the production of N(2)O by enrichment cultures of ammonia oxidizing archaea, biological mechanisms for scavenging scarce metals, and possible links between metal bioavailability and greenhouse gas fluxes in anaerobic environments where metals may be limiting due to sulfide-metal scavenging.
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Affiliation(s)
- Jennifer B. Glass
- Division of Geological and Planetary Sciences, California Institute of TechnologyPasadena, CA, USA
| | - Victoria J. Orphan
- Division of Geological and Planetary Sciences, California Institute of TechnologyPasadena, CA, USA
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20
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Rosenbaum M, Aulenta F, Villano M, Angenent LT. Cathodes as electron donors for microbial metabolism: which extracellular electron transfer mechanisms are involved? BIORESOURCE TECHNOLOGY 2011; 102:324-33. [PMID: 20688515 DOI: 10.1016/j.biortech.2010.07.008] [Citation(s) in RCA: 283] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2010] [Revised: 06/29/2010] [Accepted: 07/02/2010] [Indexed: 05/20/2023]
Abstract
This review illuminates extracellular electron transfer mechanisms that may be involved in microbial bioelectrochemical systems with biocathodes. Microbially-catalyzed cathodes are evolving for new bioprocessing applications for waste(water) treatment, carbon dioxide fixation, chemical product formation, or bioremediation. Extracellular electron transfer processes in biological anodes, were the electrode serves as electron acceptor, have been widely studied. However, for biological cathodes the question remains: what are the biochemical mechanisms for the extracellular electron transfer from a cathode (electron donor) to a microorganism? This question was approached by not only analysing the literature on biocathodes, but also by investigating known extracellular microbial oxidation reactions in environmental processes. Here, it is predicted that in direct electron transfer reactions, c-type cytochromes often together with hydrogenases play a critical role and that, in mediated electron transfer reactions, natural redox mediators, such as PQQ, will be involved in the bioelectrochemical reaction. These mechanisms are very similar to processes at the bioanode, but the components operate at different redox potentials. The biocatalyzed cathode reactions, thereby, are not necessarily energy conserving for the microorganism.
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Affiliation(s)
- Miriam Rosenbaum
- Department of Biological and Environmental Engineering, Cornell University, 214 Riley-Robb Hall, Ithaca, NY 14853, USA.
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21
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Proteogenomic and functional analysis of chromate reduction in Acidiphilium cryptum JF-5, an Fe(III)-respiring acidophile. Biometals 2010; 23:1129-38. [DOI: 10.1007/s10534-010-9360-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2010] [Accepted: 06/15/2010] [Indexed: 11/26/2022]
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22
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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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23
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Reduction of molybdate by sulfate-reducing bacteria. Biometals 2009; 22:131-9. [DOI: 10.1007/s10534-008-9198-8] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2008] [Accepted: 12/07/2008] [Indexed: 10/21/2022]
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24
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Holmes DE, O'Neil RA, Chavan MA, N'Guessan LA, Vrionis HA, Perpetua LA, Larrahondo MJ, DiDonato R, Liu A, Lovley DR. Transcriptome of Geobacter uraniireducens growing in uranium-contaminated subsurface sediments. ISME JOURNAL 2008; 3:216-30. [PMID: 18843300 DOI: 10.1038/ismej.2008.89] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
To learn more about the physiological state of Geobacter species living in subsurface sediments, heat-sterilized sediments from a uranium-contaminated aquifer in Rifle, Colorado, were inoculated with Geobacter uraniireducens, a pure culture representative of the Geobacter species that predominates during in situ uranium bioremediation at this site. Whole-genome microarray analysis comparing sediment-grown G. uraniireducens with cells grown in defined culture medium indicated that there were 1084 genes that had higher transcript levels during growth in sediments. Thirty-four c-type cytochrome genes were upregulated in the sediment-grown cells, including several genes that are homologous to cytochromes that are required for optimal Fe(III) and U(VI) reduction by G. sulfurreducens. Sediment-grown cells also had higher levels of transcripts, indicative of such physiological states as nitrogen limitation, phosphate limitation and heavy metal stress. Quantitative reverse transcription PCR showed that many of the metabolic indicator genes that appeared to be upregulated in sediment-grown G. uraniireducens also showed an increase in expression in the natural community of Geobacter species present during an in situ uranium bioremediation field experiment at the Rifle site. These results demonstrate that it is feasible to monitor gene expression of a microorganism growing in sediments on a genome scale and that analysis of the physiological status of a pure culture growing in subsurface sediments can provide insights into the factors controlling the physiology of natural subsurface communities.
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Affiliation(s)
- Dawn E Holmes
- Department of Microbiology, University of Massachusetts, Amherst, MA 01003, USA.
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25
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Moura I, Pauleta SR, Moura JJG. Enzymatic activity mastered by altering metal coordination spheres. J Biol Inorg Chem 2008; 13:1185-95. [PMID: 18719950 DOI: 10.1007/s00775-008-0414-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2008] [Accepted: 08/01/2008] [Indexed: 11/24/2022]
Abstract
Metalloenzymes control enzymatic activity by changing the characteristics of the metal centers where catalysis takes place. The conversion between inactive and active states can be tuned by altering the coordination number of the metal site, and in some cases by an associated conformational change. These processes will be illustrated using heme proteins (cytochrome c nitrite reductase, cytochrome c peroxidase and cytochrome cd1 nitrite reductase), non-heme proteins (superoxide reductase and [NiFe]-hydrogenase), and copper proteins (nitrite and nitrous oxide reductases) as examples. These examples catalyze electron transfer reactions that include atom transfer, abstraction and insertion.
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Affiliation(s)
- Isabel Moura
- REQUIMTE, Centro de Química Fina e Biotecnologia, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal.
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26
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Giedroc DP, Arunkumar AI. Metal sensor proteins: nature's metalloregulated allosteric switches. Dalton Trans 2007:3107-20. [PMID: 17637984 DOI: 10.1039/b706769k] [Citation(s) in RCA: 152] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Metalloregulatory proteins control the expression of genes that allow organisms to quickly adapt to chronic toxicity or deprivation of both biologically essential metal ions and heavy metal pollutants found in their microenvironment. Emerging evidence suggests that metal ion homeostasis and resistance defines an important tug-of-war in human host-bacterial pathogen interactions. This adaptive response originates with the formation of "metal receptor" complexes of exquisite selectivity. In this perspective, we summarize consensus structural features of metal sensing coordination complexes and the evolution of distinct metal selectivities within seven characterized metal sensor protein families. In addition, we place recent efforts to understand the structural basis of metal-induced allosteric switching of these metalloregulatory proteins in a thermodynamic framework, and review the degree to which coordination chemistry drives changes in protein structure and dynamics in selected metal sensor systems. New insights into how metal sensor proteins function in the complex intracellular milieu of the cytoplasm of cells will require a more sophisticated understanding of the "metallome" and will benefit greatly from ongoing collaborative efforts in bioinorganic, biophysical and analytical chemistry, structural biology and microbiology.
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Affiliation(s)
- David P Giedroc
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, TX 77843-2128, USA.
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