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Reginald SS, Etzerodt M, Fapyane D, Chang IS. Functional Expression of a Mo-Cu-Dependent Carbon Monoxide Dehydrogenase (CODH) and Its Use as a Dissolved CO Bio-microsensor. ACS Sens 2021; 6:2772-2782. [PMID: 34253013 DOI: 10.1021/acssensors.1c01243] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Herein, we report the heterologous expression in Escherichia coli of a Mo-Cu-containing carbon monoxide dehydrogenase (Mo-Cu CODH) from Hydrogenophaga pseudoflava, which resulted in an active protein catalyzing CO oxidation to CO2. By supplying the E. coli growth medium with Na2MoO4 (Mo) and CuSO4 (Cu), the Mo-Cu CODH metal cofactors precursors, the expressed L-subunit was found to have CO-oxidation activity even without the M- and S- subunits. This successful expression of CO-oxidizing-capable single L-subunit provides direct evidence of its role as the catalytic center of Mo-Cu CODH that has not been discovered and studied before. Subsequently, we used the expressed protein to construct a CO bio-microsensor based on a newly developed fast and sensitive Clark-type CO2 transducer using an aprotic solvent/ionic liquid electrolyte. The CO bio-microsensor exhibited a linear response to CO concentration in the 0-9 μM range, with a limit of detection (LOD) of 15 nM CO. The sensor uses a mixture of Mo-Cu CODH's L-subunit/Mo, Cu cofactors/methylene blue, confined in the enzyme chamber that is placed in front of a CO2 transducer. The optimized sensor's sensitivity and performance were retained to levels of at least 80% for 1 week of continuous polarization and operation in an aqueous medium. We have also demonstrated the use of an alkaline front-trap solution to make a completely O2/CO2 interference-free microsensor. The CO bio-microsensor developed in this study is potentially useful as an analytical tool for the detection of trace CO in dissolved form for monitoring dissolved CO concentration dynamics in natural or synthetic systems.
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Affiliation(s)
- Stacy Simai Reginald
- School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology, 261 Cheomdan-gwagiro, Buk-gu, Gwangju 61005, Republic of Korea
| | - Michael Etzerodt
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, Aarhus 8000, Denmark
| | - Deby Fapyane
- Aarhus University Centre of Water Technology (WATEC), Department of Bioscience, Aarhus University, Ny Munkegade 116, Aarhus 8000, Denmark
| | - In Seop Chang
- School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology, 261 Cheomdan-gwagiro, Buk-gu, Gwangju 61005, Republic of Korea
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Fapyane D, Berillo D, Marty JL, Revsbech NP. Urea Biosensor Based on a CO 2 Microsensor. ACS OMEGA 2020; 5:27582-27590. [PMID: 33134722 PMCID: PMC7594316 DOI: 10.1021/acsomega.0c04146] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 10/02/2020] [Indexed: 06/11/2023]
Abstract
Urea sensors based on electrodes in direct contact with the medium have limited long-term stability when exposed to complex media. Here, we present a urea biosensor based on urease immobilized in an alginate polymer, buffered at pH 6, and placed in front of a newly developed fast and sensitive CO2 microsensor, where the electrodes are shielded by a gas-permeable membrane. The CO2 produced by the urease in the presence of urea diffuses into the microsensor and is reduced at a Ag cathode. Oxygen interference is prevented by a Cr2+ trap. The 95% response time to changes in urea concentration was 120 s with a linear calibration curve in the range 0-1000 μM and a detection limit of 1 μM. The Ni2+ cofactor to improve sensor performance was continuously supplied from a reservoir behind the sensor tip. The stability of the urea sensor was optimized by the addition of bovine serum albumin as a stabilizer to the urease/alginate mixture that was cross-linked with glutaraldehyde and Ca2+ ions. This immobilization strategy resulted in about 70% of the initial urea sensor sensitivity after two weeks of continuous operation. The sensor was successfully tested in blood serum.
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Affiliation(s)
- Deby Fapyane
- Aarhus University
Centre for Water Technology (WATEC), Department of Biology, Aarhus University, Ny Munkegade 114-116, Aarhus
C 8000, Denmark
| | - Dmitriy Berillo
- Aarhus University
Centre for Water Technology (WATEC), Department of Biology, Aarhus University, Ny Munkegade 114-116, Aarhus
C 8000, Denmark
| | - Jean-Louis Marty
- BAE (Biocapteurs-Analyses-Environnement), Université de Perpignan Via Domitia, 52 Avenue Paul Alduy, Perpignan
Cedex 66860, France
| | - Niels Peter Revsbech
- Aarhus University
Centre for Water Technology (WATEC), Department of Biology, Aarhus University, Ny Munkegade 114-116, Aarhus
C 8000, Denmark
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Revsbech NP, Nielsen M, Fapyane D. Ion Selective Amperometric Biosensors for Environmental Analysis of Nitrate, Nitrite and Sulfate. SENSORS 2020; 20:s20154326. [PMID: 32756490 PMCID: PMC7435940 DOI: 10.3390/s20154326] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/27/2020] [Accepted: 07/30/2020] [Indexed: 11/18/2022]
Abstract
Inorganic ions that can be redox-transformed by living cells can be sensed by biosensors, where the redox transformation gives rise to a current in a measuring circuit. Such biosensors may be based on enzymes, or they may be based on application of whole cells. In this review focus will be on biosensors for the environmentally important ions NO3−, NO2−, and SO42−, and for comparison alternative sensor-based detection will also be mentioned. The developed biosensors are generally characterized by a high degree of specificity, but unfortunately also by relatively short lifetimes. There are several investigations where biosensor measurement of NO3− and NO2− have given new insight into the functioning of nitrogen transformations in man-made and natural environments such as sediments and biofilms, but the biosensors have not become routine tools. Future modifications resulting in better long-term stability may enable such general use.
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Affiliation(s)
- Niels Peter Revsbech
- Aarhus University Centre for Water Technology, Department of Biology, Aarhus University, Ny Munkegade 114-116, 8000 Aarhus C, Denmark;
- Correspondence: ; Tel.: +45-233-82-187
| | - Michael Nielsen
- Department of Sensor Productions, Unisense A/S, Tueager 1, 8200 Aarhus N, Denmark;
| | - Deby Fapyane
- Aarhus University Centre for Water Technology, Department of Biology, Aarhus University, Ny Munkegade 114-116, 8000 Aarhus C, Denmark;
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Martínez-Espinosa RM. Microorganisms and Their Metabolic Capabilities in the Context of the Biogeochemical Nitrogen Cycle at Extreme Environments. Int J Mol Sci 2020; 21:ijms21124228. [PMID: 32545812 PMCID: PMC7349289 DOI: 10.3390/ijms21124228] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 06/12/2020] [Indexed: 12/23/2022] Open
Abstract
Extreme microorganisms (extremophile) are organisms that inhabit environments characterized by inhospitable parameters for most live beings (extreme temperatures and pH values, high or low ionic strength, pressure, or scarcity of nutrients). To grow optimally under these conditions, extremophiles have evolved molecular adaptations affecting their physiology, metabolism, cell signaling, etc. Due to their peculiarities in terms of physiology and metabolism, they have become good models for (i) understanding the limits of life on Earth, (ii) exploring the possible existence of extraterrestrial life (Astrobiology), or (iii) to look for potential applications in biotechnology. Recent research has revealed that extremophilic microbes play key roles in all biogeochemical cycles on Earth. Nitrogen cycle (N-cycle) is one of the most important biogeochemical cycles in nature; thanks to it, nitrogen is converted into multiple chemical forms, which circulate among atmospheric, terrestrial and aquatic ecosystems. This review summarizes recent knowledge on the role of extreme microorganisms in the N-cycle in extremophilic ecosystems, with special emphasis on members of the Archaea domain. Potential implications of these microbes in global warming and nitrogen balance, as well as their biotechnological applications are also discussed.
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Affiliation(s)
- Rosa María Martínez-Espinosa
- Biochemistry and Molecular Biology Division, Agrochemistry and Biochemistry Department, Faculty of Sciences, University of Alicante, Ap. 99, E-03080 Alicante, Spain; ; Tel.: +34-965903400 (ext. 1258)
- Multidisciplinary Institute for Environmental Studies “Ramón Margalef”, University of Alicante, Ap. 99, E-03080 Alicante, Spain
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5
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Zhong XZ, Zeng Y, Wang SP, Sun ZY, Tang YQ, Kida K. Insight into the microbiology of nitrogen cycle in the dairy manure composting process revealed by combining high-throughput sequencing and quantitative PCR. BIORESOURCE TECHNOLOGY 2020; 301:122760. [PMID: 31972401 DOI: 10.1016/j.biortech.2020.122760] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 01/03/2020] [Accepted: 01/06/2020] [Indexed: 06/10/2023]
Abstract
Nitrogen cycling during composting process is not yet fully understood. This study explored the key genes involved in nitrogen cycling during dairy manure composting process using high-throughput sequencing and quantitative PCR technologies. Results showed that nitrogen fixation occurred mainly during the thermophilic and cooling phases, and significantly enhanced the nitrogen content of compost. Thermoclostridium stercorarium was the main diazotroph. Ammonia oxidation occurred during the maturation phase and Nitrosomonas sp. was the most abundant ammonia oxidizing bacteria. Denitrification contributed to the greatest nitrogen loss during the composting process. The nirK community was dominated by Luteimonas sp. and Achromobacter sp., while the nirS community was dominated by Alcaligenes faecalis and Pseudomonas stutzeri. The nosZ community varied in a succession of Halomonas ilicicola, Pseudomonas flexibili and Labrenzia alba dominated communities according to different composting phases. Based on these results, nitrogen cycling models for different phases of the dairy manure composting process were established.
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Affiliation(s)
- Xiao-Zhong Zhong
- College of Architecture and Environment, Sichuan University, Chengdu, Sichuan, China
| | - Yan Zeng
- College of Architecture and Environment, Sichuan University, Chengdu, Sichuan, China
| | - Shi-Peng Wang
- College of Architecture and Environment, Sichuan University, Chengdu, Sichuan, China
| | - Zhao-Yong Sun
- College of Architecture and Environment, Sichuan University, Chengdu, Sichuan, China.
| | - Yue-Qin Tang
- College of Architecture and Environment, Sichuan University, Chengdu, Sichuan, China
| | - Kenji Kida
- College of Architecture and Environment, Sichuan University, Chengdu, Sichuan, China
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Cuartero M, Crespo G, Cherubini T, Pankratova N, Confalonieri F, Massa F, Tercier-Waeber ML, Abdou M, Schäfer J, Bakker E. In Situ Detection of Macronutrients and Chloride in Seawater by Submersible Electrochemical Sensors. Anal Chem 2018. [DOI: 10.1021/acs.analchem.7b05299] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Maria Cuartero
- Department of Inorganic and Analytical Chemistry, University of Geneva, Quai Ernest-Ansermet 30, CH-1211 Geneva, Switzerland
| | - Gaston Crespo
- Department of Inorganic and Analytical Chemistry, University of Geneva, Quai Ernest-Ansermet 30, CH-1211 Geneva, Switzerland
| | - Thomas Cherubini
- Department of Inorganic and Analytical Chemistry, University of Geneva, Quai Ernest-Ansermet 30, CH-1211 Geneva, Switzerland
| | - Nadezda Pankratova
- Department of Inorganic and Analytical Chemistry, University of Geneva, Quai Ernest-Ansermet 30, CH-1211 Geneva, Switzerland
| | | | - Francesco Massa
- Department of Earth, Environment and Life Sciences, University of Genoa, C.so Europa 26, 16132 Genoa, Italy
| | - Mary-Lou Tercier-Waeber
- Department of Inorganic and Analytical Chemistry, University of Geneva, Quai Ernest-Ansermet 30, CH-1211 Geneva, Switzerland
| | - Melina Abdou
- UMR CNRS 5805 EPOC, Université de Bordeaux, Bat 18, Allée Geoffroy Saint-Hilaire, 33615 Pessac, France
| | - Jörg Schäfer
- UMR CNRS 5805 EPOC, Université de Bordeaux, Bat 18, Allée Geoffroy Saint-Hilaire, 33615 Pessac, France
| | - Eric Bakker
- Department of Inorganic and Analytical Chemistry, University of Geneva, Quai Ernest-Ansermet 30, CH-1211 Geneva, Switzerland
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Sveegaard SG, Nielsen M, Andersen MH, Gothelf KV. Phosphines as Efficient Dioxygen Scavengers in Nitrous Oxide Sensors. ACS Sens 2017; 2:695-702. [PMID: 28723161 DOI: 10.1021/acssensors.7b00152] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A current challenge for development of amperometric sensors for the greenhouse gas nitrous oxide (N2O) is their sensitivity toward dioxygen and trace water. The need for aqueous dioxygen scavengers in front of the sensor implies a background signal from penetrating water vapor. In this paper, we introduce substituted phosphines as dioxygen scavengers and demonstrate the application in a dioxygen-insensitive N2O sensor. Suitably substituted phosphines have been synthesized to achieve good solubility properties in the electrochemically inert solvent propylene carbonate. Several sensors with and without physical separation of the sensing and dioxygen scavenging compartments were made and compared to current commercial sensors. The use of phosphines soluble in organic solvents as dioxygen scavengers yielded a higher sensitivity, albeit with longer response time. Proof-of-concept N2O sensors without the physically separated dioxygen scavenger chamber showed a greatly enhanced sensitivity with a comparable response time, thus demonstrating the possibility for greatly simplified sensor construction.
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Affiliation(s)
- Steffen Gralert Sveegaard
- Danish
National Research Foundation: Center for DNA Nanotechnology, Interdisciplinary
Nanoscience Center (iNANO) and Department of Chemistry, Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark
- Unisense Environment A/S, Tueager
1, DK-8200 Aarhus N, Denmark
| | | | | | - Kurt Vesterager Gothelf
- Danish
National Research Foundation: Center for DNA Nanotechnology, Interdisciplinary
Nanoscience Center (iNANO) and Department of Chemistry, Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark
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8
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Jabeen G, Farooq R. Microbial Fuel Cells and Their Applications for Cost Effective Water Pollution Remediation. ACTA ACUST UNITED AC 2015. [DOI: 10.1007/s40011-015-0683-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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9
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Liu W, Gu Y, Sun G, Na K, Li C, Tang L, Zhang Z, Yang M. Poly(diallydimethylammonium chloride) Functionalized Graphene/Double-walled Carbon Nanotube Composite for Amperometric Determination of Nitrite. ELECTROANAL 2015. [DOI: 10.1002/elan.201500358] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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10
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Mistry KK, Layek K, Mahapatra A, RoyChaudhuri C, Saha H. A review on amperometric-type immunosensors based on screen-printed electrodes. Analyst 2015; 139:2289-311. [PMID: 24678518 DOI: 10.1039/c3an02050a] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this brief review, we summarize the recent research activities involved in the development of amperometric-type immunosensors based on screen-printed electrodes (SPEs). We focus on the underlying principle involved in these types of sensors, their fabrication and electrode surface modification. We also discuss the various factors involved in the designing of such immunosensors and how they affect their performances. Finally we provide an insight into the drawbacks associated with these SPEs.
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Affiliation(s)
- Kalyan Kumar Mistry
- CSIR-Central Mechanical Engineering Research Institute, M. G. Avenue, Durgapur-713209, India.
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11
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Anaerobic methane oxidation coupled to denitrification is the dominant methane sink in a deep lake. Proc Natl Acad Sci U S A 2014; 111:18273-8. [PMID: 25472842 DOI: 10.1073/pnas.1411617111] [Citation(s) in RCA: 125] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Anaerobic methane oxidation coupled to denitrification, also known as "nitrate/nitrite-dependent anaerobic methane oxidation" (n-damo), was discovered in 2006. Since then, only a few studies have identified this process and the associated microorganisms in natural environments. In aquatic sediments, the close proximity of oxygen- and nitrate-consumption zones can mask n-damo as aerobic methane oxidation. We therefore investigated the vertical distribution and the abundance of denitrifying methanotrophs related to Candidatus Methylomirabilis oxyfera with cultivation-independent molecular techniques in the sediments of Lake Constance. Additionally, the vertical distribution of methane oxidation and nitrate consumption zones was inferred from high-resolution microsensor profiles in undisturbed sediment cores. M. oxyfera-like bacteria were virtually absent at shallow-water sites (littoral sediment) and were very abundant at deep-water sites (profundal sediment). In profundal sediment, the vertical distribution of M. oxyfera-like bacteria showed a distinct peak in anoxic layers that coincided with the zone of methane oxidation and nitrate consumption, a strong indication for n-damo carried out by M. oxyfera-like bacteria. Both potential n-damo rates calculated from cell densities (660-4,890 µmol CH4⋅m(-2)⋅d(-1)) and actual rates calculated from microsensor profiles (31-437 µmol CH4⋅m(-2)⋅d(-1)) were sufficiently high to prevent methane release from profundal sediment solely by this process. Additionally, when nitrate was added to sediment cores exposed to anoxic conditions, the n-damo zone reestablished well below the sediment surface, completely preventing methane release from the sediment. We conclude that the previously overlooked n-damo process can be the major methane sink in stable freshwater environments if nitrate is available in anoxic zones.
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12
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Carlisle E, Yarnes C, Toney MD, Bloom AJ. Nitrate reductase (15)N discrimination in Arabidopsis thaliana, Zea mays, Aspergillus niger, Pichea angusta, and Escherichia coli. FRONTIERS IN PLANT SCIENCE 2014; 5:317. [PMID: 25071800 PMCID: PMC4078254 DOI: 10.3389/fpls.2014.00317] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Accepted: 06/15/2014] [Indexed: 05/06/2023]
Abstract
Stable (15)N isotopes have been used to examine movement of nitrogen (N) through various pools of the global N cycle. A central reaction in the cycle involves the reduction of nitrate (NO(-) 3) to nitrite (NO(-) 2) catalyzed by nitrate reductase (NR). Discrimination against (15)N by NR is a major determinant of isotopic differences among N pools. Here, we measured in vitro (15)N discrimination by several NRs purified from plants, fungi, and a bacterium to determine the intrinsic (15)N discrimination by the enzyme and to evaluate the validity of measurements made using (15)N-enriched NO(-) 3. Observed NR isotope discrimination ranged from 22 to 32‰ (kinetic isotope effects of 1.022-1.032) among the different isozymes at natural abundance (15)N (0.37%). As the fractional (15)N content of substrate NO(-) 3 increased from natural abundance, the product (15)N fraction deviated significantly from that expected based on substrate enrichment and (15)N discrimination measured at natural abundance. Additionally, isotopic discrimination by denitrifying bacteria used to reduce NO(-) 3 and NO(-) 2 in some protocols became a greater source of error as (15)N enrichment increased. We briefly discuss potential causes of the experimental artifacts with enriched (15)N and recommend against the use of highly enriched (15)N tracers to study N discrimination in plants or soils.
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Affiliation(s)
- Eli Carlisle
- Department of Plant Sciences, University of CaliforniaDavis, CA, USA
| | - Chris Yarnes
- Department of Plant Sciences, University of CaliforniaDavis, CA, USA
| | | | - Arnold J. Bloom
- Department of Plant Sciences, University of CaliforniaDavis, CA, USA
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13
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Xu J, Jiang B, Xie J, Xiang Y, Yuan R, Chai Y. Sensitive point-of-care monitoring of HIV related DNA sequences with a personal glucometer. Chem Commun (Camb) 2013; 48:10733-5. [PMID: 23011391 DOI: 10.1039/c2cc35941c] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The hybridizations between the HIV target DNA and the capture probes as well as the signal probes conjugated to the multi-invertase/nanoparticle composites lead to the conversion of sucrose to glucose, which is monitored by the personal glucometer and provides quantitative digital readings for point-of-care diagnosis of HIV DNA fragments.
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Affiliation(s)
- Jin Xu
- Key Laboratory on Luminescence and Real-Time Analysis, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
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14
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Gao ZF, Gao JB, Zhou LY, Zhang Y, Si JC, Luo HQ, Li NB. Rapid assembly of ssDNA on gold electrode surfaces at low pH and high salt concentration conditions. RSC Adv 2013. [DOI: 10.1039/c3ra40810h] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
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15
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Almeida MG, Serra A, Silveira CM, Moura JJ. Nitrite biosensing via selective enzymes--a long but promising route. SENSORS (BASEL, SWITZERLAND) 2010; 10:11530-55. [PMID: 22163541 PMCID: PMC3231041 DOI: 10.3390/s101211530] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2010] [Revised: 11/19/2010] [Accepted: 12/06/2010] [Indexed: 12/21/2022]
Abstract
The last decades have witnessed a steady increase of the social and political awareness for the need of monitoring and controlling environmental and industrial processes. In the case of nitrite ion, due to its potential toxicity for human health, the European Union has recently implemented a number of rules to restrict its level in drinking waters and food products. Although several analytical protocols have been proposed for nitrite quantification, none of them enable a reliable and quick analysis of complex samples. An alternative approach relies on the construction of biosensing devices using stable enzymes, with both high activity and specificity for nitrite. In this paper we review the current state-of-the-art in the field of electrochemical and optical biosensors using nitrite reducing enzymes as biorecognition elements and discuss the opportunities and challenges in this emerging market.
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Affiliation(s)
- M. Gabriela Almeida
- REQUIMTE—Departmento de Química, Faculdade de Ciencias e Tecnologia (UNL), 2829-516 Monte Caparica, Portugal; E-Mails: (A.S.); (C.M.S.); (J.J.G.M.)
- Escola Superior de Saude Egas Moniz, Campus Universitario, Quinta da Granja, 2829-511 Monte Caparica, Portugal
| | - Alexandra Serra
- REQUIMTE—Departmento de Química, Faculdade de Ciencias e Tecnologia (UNL), 2829-516 Monte Caparica, Portugal; E-Mails: (A.S.); (C.M.S.); (J.J.G.M.)
| | - Celia M. Silveira
- REQUIMTE—Departmento de Química, Faculdade de Ciencias e Tecnologia (UNL), 2829-516 Monte Caparica, Portugal; E-Mails: (A.S.); (C.M.S.); (J.J.G.M.)
| | - Jose J.G. Moura
- REQUIMTE—Departmento de Química, Faculdade de Ciencias e Tecnologia (UNL), 2829-516 Monte Caparica, Portugal; E-Mails: (A.S.); (C.M.S.); (J.J.G.M.)
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16
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Deng L, Guo S, Liu Z, Zhou M, Li D, Liu L, Li G, Wang E, Dong S. To boost c-type cytochrome wire efficiency of electrogenic bacteria with Fe3O4/Au nanocomposites. Chem Commun (Camb) 2010; 46:7172-4. [DOI: 10.1039/c0cc01371d] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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17
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Erable B, Duţeanu NM, Ghangrekar M, Dumas C, Scott K. Application of electro-active biofilms. BIOFOULING 2010; 26:57-71. [PMID: 20390557 DOI: 10.1080/08927010903161281] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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18
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Sequence-specific detection of trace DNA via a junction-probe electrochemical sensor employed template-enhanced hybridization strategy. Biosens Bioelectron 2009; 25:815-9. [DOI: 10.1016/j.bios.2009.08.032] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2009] [Revised: 08/20/2009] [Accepted: 08/21/2009] [Indexed: 11/24/2022]
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19
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Moore TS, Mullaugh KM, Holyoke RR, Madison AS, Yücel M, Luther GW. Marine chemical technology and sensors for marine waters: potentials and limits. ANNUAL REVIEW OF MARINE SCIENCE 2009; 1:91-115. [PMID: 21141031 DOI: 10.1146/annurev.marine.010908.163817] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
A significant need exists for in situ sensors that can measure chemical species involved in the major processes of primary production (photosynthesis and chemosynthesis) and respiration. Some key chemical species are O2, nutrients (N and P), micronutrients (metals), pCO2, dissolved inorganic carbon (DIC), pH, and sulfide. Sensors need to have excellent detection limits, precision, selectivity, response time, a large dynamic concentration range, low power consumption, robustness, and less variation of instrument response with temperature and pressure, as well as be free from fouling problems (biological, physical, and chemical). Here we review the principles of operation of most sensors used in marine waters. We also show that some sensors can be used in several different oceanic environments to detect the target chemical species, whereas others are useful in only one environment because of various limitations. Several sensors can be used truly in situ, whereas many others involve water brought into a flow cell via tubing to the analyzer in the environment or aboard ship. Multi-element sensors that measure many chemical species in the same water mass should be targeted for further development.
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Affiliation(s)
- Tommy S Moore
- College of Marine and Earth Studies, University of Delaware, Lewes, Delaware 19958, USA.
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Morgan-Sagastume F, Nielsen JL, Nielsen PH. Substrate-dependent denitrification of abundant probe-defined denitrifying bacteria in activated sludge. FEMS Microbiol Ecol 2008; 66:447-61. [DOI: 10.1111/j.1574-6941.2008.00571.x] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Martínez-García M, Stief P, Díaz-Valdés M, Wanner G, Ramos-Esplá A, Dubilier N, Antón J. Ammonia-oxidizing Crenarchaeota and nitrification inside the tissue of a colonial ascidian. Environ Microbiol 2008; 10:2991-3001. [PMID: 18793310 DOI: 10.1111/j.1462-2920.2008.01761.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Marine Crenarchaeota represent an abundant component of the oceanic microbiota that play an important role in the global nitrogen cycle. Here we report the association of the colonial ascidian Cystodytes dellechiajei with putative ammonia-oxidizing Crenarchaeota that could actively be involved in nitrification inside the animal tissue. As shown by 16S rRNA gene analysis, the ascidian-associated Crenarchaeota were phylogenetically related to Nitrosopumilus maritimus, the first marine archaeon isolated in pure culture that grows chemolithoautotrophically oxidizing ammonia to nitrite aerobically. Catalysed reporter deposition (CARD)-FISH revealed that the Crenarchaeota were specifically located inside the tunic tissue of the colony, where moreover the expression of amoA gene was detected. The amoA gene encodes the alpha-subunit of ammonia monooxygenase, which is involved in the first step of nitrification, the oxidation of ammonia to nitrite. Sequencing of amoA gene showed that they were phylogenetically related to amoA genes of N. maritimus and other putative ammonia-oxidizing marine Crenarchaeota. In order to track the suspected nitrification activity inside the ascidian colony under in vivo conditions, microsensor profiles were measured through the tunic tissue. Net NO(x) production was detected in the tunic layer 1200-1800 microm with rates of 58-90 nmol cm(-3) h(-1). Oxygen and pH microsensor profiles showed that the layer of net NO(x) production coincided with O(2) concentrations of 103-116 microM and pH value of 5.2. Together, molecular and microsensor data indicate that Crenarchaeota could oxidize ammonia to nitrite aerobically, and thus be involved in nitrification inside the ascidian tissue.
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Impact of nitrate on the structure and function of bacterial biofilm communities in pipelines used for injection of seawater into oil fields. Appl Environ Microbiol 2008; 74:2841-51. [PMID: 18344353 DOI: 10.1128/aem.02027-07] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We studied the impact of NO(3)(-) on the bacterial community composition, diversity, and function in in situ industrial, anaerobic biofilms by combining microsensor profiling, (15)N and (35)S labeling, and 16S rRNA gene-based fingerprinting. Biofilms were grown on carbon steel coupons within a system designed to treat seawater for injection into an oil field for pressurized oil recovery. NO(3)(-) was added to the seawater in an attempt to prevent bacterial H(2)S generation and microbially influenced corrosion in the field. Microprofiling of nitrogen compounds and redox potential inside the biofilms showed that the zone of highest metabolic activity was located close to the metal surface, correlating with a high bacterial abundance in this zone. Upon addition, NO(3)(-) was mainly reduced to NO(2)(-). In biofilms grown in the absence of NO(3)(-), redox potentials of <-450 mV at the metal surface suggested the release of Fe(2+). NO(3)(-) addition to previously untreated biofilms induced a decline (65%) in bacterial species richness, with Methylophaga- and Colwellia-related sequences having the highest number of obtained clones in the clone library. In contrast, no changes in community composition and potential NO(3)(-) reduction occurred upon subsequent withdrawal of NO(3)(-). Active sulfate reduction was below detection levels in all biofilms, but S isotope fractionation analysis of sulfide deposits suggested that it must have occurred either at low rates or episodically. Scanning electron microscopy revealed that pitting corrosion occurred on all coupons, independent of the treatment. However, uniform corrosion was clearly mitigated by NO(3)(-) addition.
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Revsbech NP, Risgaard-Petersen N, Schramm A, Nielsen LP. Nitrogen transformations in stratified aquatic microbial ecosystems. Antonie van Leeuwenhoek 2006; 90:361-75. [PMID: 17033881 DOI: 10.1007/s10482-006-9087-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2006] [Accepted: 05/11/2006] [Indexed: 10/24/2022]
Abstract
New analytical methods such as advanced molecular techniques and microsensors have resulted in new insights about how nitrogen transformations in stratified microbial systems such as sediments and biofilms are regulated at a microm-mm scale. A large and ever-expanding knowledge base about nitrogen fixation, nitrification, denitrification, and dissimilatory reduction of nitrate to ammonium, and about the microorganisms performing the processes, has been produced by use of these techniques. During the last decade the discovery of anammmox bacteria and migrating, nitrate accumulating bacteria performing dissimilatory reduction of nitrate to ammonium have given new dimensions to the understanding of nitrogen cycling in nature, and the occurrence of these organisms and processes in stratified microbial communities will be described in detail.
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Affiliation(s)
- Niels Peter Revsbech
- Institute of Biological Sciences, Microbiology, University of Aarhus, bd. 540, DK-8000, Aarhus C, Denmark.
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Köster M, Gliesche CG, Wardenga R. Microbiosensors for measurement of microbially available dissolved organic carbon: sensor characteristics and preliminary environmental application. Appl Environ Microbiol 2006; 72:7063-73. [PMID: 16936058 PMCID: PMC1636147 DOI: 10.1128/aem.00641-06] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Microbial respiration-based microbiosensors used for quantification of available dissolved organic carbon (ADOC) instantaneously respired by microorganisms are described. The sensing membranes contained aerobic seawater microorganisms immobilized in a polyurethane hydrogel. Molecular investigations revealed that the bacterial strain used was most closely related to Staphylococcus warneri. This strain was characterized by low substrate selectivity, which was reflected in the response to various mono- and disaccharides, short-chain fatty acids, and amino acids, as determined using Biolog microplates. Specific emphasis was placed on critically assessing biosensor functioning that was affected by preconditioning of the selected bacterial strain, chemical and geometric properties of the sensing membrane (e.g., composition, permeability, and thickness), and the distribution, biomass, and physiological state of immobilized cells, as well as the exposure conditions (e.g., temperature and nutrient supply). The sensors revealed that there was a linear response up to a glucose concentration of 500 microM depending on the type, characteristics, and recent history of the sensors. The detection limit of the sensors was equivalent to about 6 to 10 microM glucose. The 90% response time ranged from 1 to 5 min. Generally, the response of the biosensors became weaker with time. The shelf lives of individual sensors were up to 2 weeks. Measurements based on optical ADOC microbiosensors revealed that in photoautotrophically dominated sandy coastal sediments, the pool sizes and turnover of ADOC were regulated by the photosynthetic activity of benthic microalgae and microbial aerobic respiration. A large increase in ADOC production was observed shortly after the microphytobenthic primary production reached the maximum value at midday, whereas ADOC was consumed by microbial respiration during the night.
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Affiliation(s)
- Marion Köster
- Institut für Okologie der Ernst-Moritz-Arndt-Universität Greifswald, Schwedenhagen 6, 18565 Kloster/Hiddensee, Germany.
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Bjerketorp J, Håkansson S, Belkin S, Jansson JK. Advances in preservation methods: keeping biosensor microorganisms alive and active. Curr Opin Biotechnol 2006; 17:43-9. [PMID: 16368231 DOI: 10.1016/j.copbio.2005.12.005] [Citation(s) in RCA: 121] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2005] [Revised: 11/05/2005] [Accepted: 12/07/2005] [Indexed: 11/24/2022]
Abstract
The ability of bacteria to sense their surroundings can be employed to measure the bioavailability and toxicity of pollutants. However, long-term maintenance of both viability and activity of the sensor bacteria is required for the development of cell-based devices for environmental monitoring. To meet these demands, various techniques to conserve such bacteria have been reported, including freeze drying, vacuum drying, continuous cultivation, and immobilisation in biocompatible polymers of organic or inorganic origin. Much effort has been invested in merging these bacterial preservation schemes with the construction of sensor cell arrays on platforms such as biochips or optic fibres, hopefully leading to effective miniaturised whole-cell biosensor systems. These approaches hold much promise for the future. Nevertheless, their eventual implementation in practical devices calls for significant enhancement of current knowledge on formulation of reporter microorganisms.
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Affiliation(s)
- Joakim Bjerketorp
- Department of Microbiology, Swedish University of Agricultural Sciences (SLU), Box 7025, SE-750 07 Uppsala, Sweden.
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Meyer RL, Risgaard-Petersen N, Allen DE. Correlation between anammox activity and microscale distribution of nitrite in a subtropical mangrove sediment. Appl Environ Microbiol 2005; 71:6142-9. [PMID: 16204532 PMCID: PMC1265924 DOI: 10.1128/aem.71.10.6142-6149.2005] [Citation(s) in RCA: 158] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The distribution of anaerobic ammonium oxidation (anammox) in nature has been addressed by only a few environmental studies, and our understanding of how anammox bacteria compete for substrates in natural environments is therefore limited. In this study, we measure the potential anammox rates in sediment from four locations in a subtropical tidal river system. Porewater profiles of NO(x)(-) (NO2- plus NO3-) and NO2- were measured with microscale biosensors, and the availability of NO2- was compared with the potential for anammox activity. The potential rate of anammox increased with increasing distance from the mouth of the river and correlated strongly with the production of nitrite in the sediment and with the average concentration or total pool of nitrite in the suboxic sediment layer. Nitrite accumulated both from nitrification and from NO(x)(-) reduction, though NO(x)(-) reduction was shown to have the greatest impact on the availability of nitrite in the suboxic sediment layer. This finding suggests that denitrification, though using NO2- as a substrate, also provides a substrate for the anammox process, which has been suggested in previous studies where microscale NO2- profiles were not measured.
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Affiliation(s)
- Rikke Louise Meyer
- Advanced Wastewater Management Centre, The University of Queensland, St. Lucia, QLD 4072, Australia.
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Sliekers AO, Haaijer SCM, Stafsnes MH, Kuenen JG, Jetten MSM. Competition and coexistence of aerobic ammonium- and nitrite-oxidizing bacteria at low oxygen concentrations. Appl Microbiol Biotechnol 2005; 68:808-17. [PMID: 15818474 DOI: 10.1007/s00253-005-1974-6] [Citation(s) in RCA: 97] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2005] [Revised: 03/16/2005] [Accepted: 03/20/2005] [Indexed: 10/25/2022]
Abstract
In natural and man-made ecosystems nitrifying bacteria experience frequent exposure to oxygen-limited conditions and thus have to compete for oxygen. In several reactor systems (retentostat, chemostat and sequencing batch reactors) it was possible to establish co-cultures of aerobic ammonium- and nitrite-oxidizing bacteria at very low oxygen concentrations (2-8 microM) provided that ammonium was the limiting N compound. When ammonia was in excess of oxygen, the nitrite-oxidizing bacteria were washed out of the reactors, and ammonium was converted to mainly nitrite, nitric oxide and nitrous oxide by Nitrosomonas-related bacteria. The situation could be rapidly reversed by adjusting the oxygen to ammonium ratio in the reactor. In batch and continuous tests, no inhibitory effect of ammonium, nitric oxide or nitrous oxide on nitrite-oxidizing bacteria could be detected in our studies. The recently developed oxygen microsensors may be helpful to determine the kinetic parameters of the nitrifying bacteria, which are needed to make predictive kinetic models of their competition.
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Affiliation(s)
- A Olav Sliekers
- Department of Biotechnology, Faculty of Applied Science, Delft University of Technology, Julianalaan 67, 2628 BC, Delft, The Netherlands
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Meyer RL, Zeng RJ, Giugliano V, Blackall LL. Challenges for simultaneous nitrification, denitrification, and phosphorus removal in microbial aggregates: mass transfer limitation and nitrous oxide production. FEMS Microbiol Ecol 2005; 52:329-38. [PMID: 16329918 DOI: 10.1016/j.femsec.2004.11.011] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2004] [Revised: 10/15/2004] [Accepted: 11/18/2004] [Indexed: 11/25/2022] Open
Abstract
The microbial community composition and activity was investigated in aggregates from a lab-scale bioreactor, in which nitrification, denitrification and phosphorus removal occurred simultaneously. The biomass was highly enriched for polyphosphate accumulating organisms facilitating complete removal of phosphorus from the bulk liquid; however, some inorganic nitrogen still remained at the end of the reactor cycle. This was ascribed to incomplete coupling of nitrification and denitrification causing NO(3)(-) accumulation. After 2 h of aeration, denitrification was dependent on the activity of nitrifying bacteria facilitating the formation of anoxic zones in the aggregates; hence, denitrification could not occur without simultaneous nitrification towards the end of the reactor cycle. Nitrous oxide was identified as a product of denitrification, when based on stored PHA as carbon source. This observation is of critical importance to the outlook of applying PHA-driven denitrification in activated sludge processes.
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Affiliation(s)
- Rikke Louise Meyer
- Advanced Wastewater Management Centre, The University of Queensland, Building 64A, Research Road, Qld 4072, Australia.
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Revsbech NP. Analysis of microbial communities with electrochemical microsensors and microscale biosensors. Methods Enzymol 2005; 397:147-66. [PMID: 16260290 DOI: 10.1016/s0076-6879(05)97009-2] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Electrochemical microsensors for O2, pH, H2S, H2, and N2O are now available commercially, thus it has become a relatively simple task to analyze the microenvironment in stratified microbial communities for several chemical species. In addition, sensors are available for the physical parameters diffusivity and flow, and based on knowledge about both transport processes and microdistribution of chemistry, it becomes possible to calculate the spatial distribution and local rates of transformations, such as aerobic respiration or denitrification. As compared to other advanced techniques, microsensor equipment is inexpensive. For example, it is possible to start working with oxygen microsensors with an investment of only about 5000 dollars. Construction of one's own microsensors is only recommended for the very dedicated user, but the investment here is mainly in terms of man-hours as the equipment is simple and inexpensive. By establishing a microsensor construction facility, it is possible to work with short-lived sensors such as ion-selective microsensors for H+, NO2(-), NO3(-), Ca2+, and CO3(-) based on ion exchangers and with microscale biosensors for NO(x)-, NO2(-), CH4, and volatile fatty acids based on immobilized bacteria.
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Affiliation(s)
- Niels Peter Revsbech
- Department of Microbial Ecology, Institute of Biology, University of Aarhus, Denmark
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