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Wheeler JHR, Foster KR, Durham WM. Individual bacterial cells can use spatial sensing of chemical gradients to direct chemotaxis on surfaces. Nat Microbiol 2024; 9:2308-2322. [PMID: 39227714 PMCID: PMC11371657 DOI: 10.1038/s41564-024-01729-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 05/10/2024] [Indexed: 09/05/2024]
Abstract
Swimming bacteria navigate chemical gradients using temporal sensing to detect changes in concentration over time. Here we show that surface-attached bacteria use a fundamentally different mode of sensing during chemotaxis. We combined microfluidic experiments, massively parallel cell tracking and fluorescent reporters to study how Pseudomonas aeruginosa senses chemical gradients during pili-based 'twitching' chemotaxis on surfaces. Unlike swimming cells, we found that temporal changes in concentration did not induce motility changes in twitching cells. We then quantified the chemotactic behaviour of stationary cells by following changes in the sub-cellular localization of fluorescent proteins as cells are exposed to a gradient that alternates direction. These experiments revealed that P. aeruginosa cells can directly sense differences in concentration across the lengths of their bodies, even in the presence of strong temporal fluctuations. Our work thus overturns the widely held notion that bacterial cells are too small to directly sense chemical gradients in space.
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Affiliation(s)
- James H R Wheeler
- Department of Physics and Astronomy, University of Sheffield, Sheffield, UK
- Department of Biology, University of Oxford, Oxford, UK
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Kevin R Foster
- Department of Biology, University of Oxford, Oxford, UK.
- Department of Biochemistry, University of Oxford, Oxford, UK.
| | - William M Durham
- Department of Physics and Astronomy, University of Sheffield, Sheffield, UK.
- Department of Biology, University of Oxford, Oxford, UK.
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2
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Guliy OI, Karavaeva OA, Smirnov AV, Eremin SA, Bunin VD. Optical Sensors for Bacterial Detection. SENSORS (BASEL, SWITZERLAND) 2023; 23:9391. [PMID: 38067765 PMCID: PMC10708710 DOI: 10.3390/s23239391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 11/12/2023] [Accepted: 11/20/2023] [Indexed: 12/18/2023]
Abstract
Analytical devices for bacterial detection are an integral part of modern laboratory medicine, as they permit the early diagnosis of diseases and their timely treatment. Therefore, special attention is directed to the development of and improvements in monitoring and diagnostic methods, including biosensor-based ones. A promising direction in the development of bacterial detection methods is optical sensor systems based on colorimetric and fluorescence techniques, the surface plasmon resonance, and the measurement of orientational effects. This review shows the detecting capabilities of these systems and the promise of electro-optical analysis for bacterial detection. It also discusses the advantages and disadvantages of optical sensor systems and the prospects for their further improvement.
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Affiliation(s)
- Olga I. Guliy
- Institute of Biochemistry and Physiology of Plants and Microorganisms—Subdivision of the Federal State Budgetary Research Institution Saratov Federal Scientific Centre of the Russian Academy of Sciences (IBPPM RAS), Saratov 410049, Russia;
| | - Olga A. Karavaeva
- Institute of Biochemistry and Physiology of Plants and Microorganisms—Subdivision of the Federal State Budgetary Research Institution Saratov Federal Scientific Centre of the Russian Academy of Sciences (IBPPM RAS), Saratov 410049, Russia;
| | - Andrey V. Smirnov
- Kotelnikov Institute of Radio Engineering and Electronics, Russian Academy of Sciences, Moscow 125009, Russia;
| | - Sergei A. Eremin
- Department of Chemistry, M. V. Lomonosov Moscow State University, Moscow 119991, Russia;
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3
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Wu CC, Wang CJ, Chang CLT, Shiku H, Wang YR, Yan JD, Ding SJ. Dissolved Oxygen-Sensing Chip Integrating an Open Container Connected with a Position-Raised Channel for Estimation of Cellular Mitochondrial Activity. ACS Sens 2022; 7:1808-1818. [PMID: 35748570 DOI: 10.1021/acssensors.1c02287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The measurement of oxygen consumption of adherent cells is a profoundly important issue for estimating the bioenergetic health and metabolism activity of cells. The study describes the construction of a microfluidic chip consisting of an open container connected with a position-raised channel and dissolved oxygen (DO)-sensing gold ultramicroelectrodes for quantifying the oxygen consumption rate (OCR) of adherent cells. The microfluidic chip design can reduce the action of shear force on the adherent cells during medium replacement. The residual concentration of analytes in the open container was only 4.4% after solution replacement via the position-raised channel. The DO reduction current measured by ultramicroelectrodes averaged in the range of 40-60 s presented high reproducibility with a 1.1% relative standard deviation suitable for OCR calculation. After short-term (90 min) cultivation, the microfluidic chip can monitor the time-dependent change in the OCR of 3T3-L1 cells for several hours by repeatedly replacing the culture medium or with the stimulation of different mitochondrial inhibitors. The presented microfluidic cell-based chip has great promise for drug screening and chemosensitivity testing by measuring OCR to evaluate the mitochondrial function of adherent cells.
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Affiliation(s)
- Ching-Chou Wu
- Department of Bio-Industrial Mechatronics Engineering, National Chung Hsing University, Taichung City 402, Taiwan.,Innovation and Development Center of Sustainable Agriculture, National Chung Hsing University, Taichung City 402, Taiwan
| | - Chieh-Jen Wang
- Department of Bio-Industrial Mechatronics Engineering, National Chung Hsing University, Taichung City 402, Taiwan
| | | | - Hitoshi Shiku
- Graduate School of Engineering, Tohoku University, 6-6-11 Aramaki-aza Aoba, Aoba-ku, Sendai 980-8579, Japan
| | - Yu-Ren Wang
- Department of Bio-Industrial Mechatronics Engineering, National Chung Hsing University, Taichung City 402, Taiwan
| | - Jia-De Yan
- Department of Bio-Industrial Mechatronics Engineering, National Chung Hsing University, Taichung City 402, Taiwan
| | - Shinn-Jyh Ding
- Department of Dentistry, Chung Shan Medical University Hospital, Taichung City 402, Taiwan, ROC.,Institute of Oral Science, Chung Shan Medical University, Taichung City 402, Taiwan
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4
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Abstract
Microbial biofilms have caused serious concerns in healthcare, medical, and food industries because of their intrinsic resistance against conventional antibiotics and cleaning procedures and their capability to firmly adhere on surfaces for persistent contamination. These global issues strongly motivate researchers to develop novel methodologies to investigate the kinetics underlying biofilm formation, to understand the response of the biofilm with different chemical and physical treatments, and to identify biofilm-specific drugs with high-throughput screenings. Meanwhile microbial biofilms can also be utilized positively as sensing elements in cell-based sensors due to their strong adhesion on surfaces. In this perspective, we provide an overview on the connections between sensing and microbial biofilms, focusing on tools used to investigate biofilm properties, kinetics, and their response to chemicals or physical agents, and biofilm-based sensors, a type of biosensor using the bacterial biofilm as a biorecognition element to capture the presence of the target of interest by measuring the metabolic activity of the immobilized microbial cells. Finally we discuss possible new research directions for the development of robust and rapid biofilm related sensors with high temporal and spatial resolutions, pertinent to a wide range of applications.
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Affiliation(s)
- Riccardo Funari
- Dipartimento di Fisica “M. Merlin”, Università degli Studi di Bari Aldo Moro, Via Amendola, 173, Bari 70125, Italy
- CNR, Istituto di Fotonica e Nanotecnologie, Via Amendola, 173, 70125 Bari, Italy
| | - Amy Q. Shen
- Micro/Bio/Nanofluidics Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan
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5
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Abstract
O2 is a fundamental environmental metabolite that affects all life on earth. While toxic to many microbes and obligately required by others, those that have appropriate physiological responses survive and can even benefit from various levels of O2, particularly in biofilm communities. Although most studies have focused on measuring O2 within biofilms, little is known about O2 gradients surrounding biofilms. Here, we developed electrochemical methodology based on scanning electrochemical microscopy to measure the O2 gradients surrounding biofilms in real time on the micron scale. Our results reveal that P. aeruginosa biofilms produce a hypoxic zone that can extend hundreds of microns from the biofilm surface and that this gradient remains even after the addition of antibiotic concentrations that eradicated 99% of viable cells. Our results provide a high resolution of the O2 gradients produced by P. aeruginosa biofilms and reveal sustained O2 consumption in the presence of antibiotics. Bacteria alter their local chemical environment through both consumption and the production of a variety of molecules, ultimately shaping the local ecology. Molecular oxygen (O2) is a key metabolite that affects the physiology and behavior of virtually all bacteria, and its consumption often results in O2 gradients within sessile bacterial communities (biofilms). O2 plays a critical role in several bacterial phenotypes, including antibiotic tolerance; however, our understanding of O2 levels within and surrounding biofilms has been hampered by the difficulties in measuring O2 levels in real-time for extended durations and at the micron scale. Here, we developed electrochemical methodology based on scanning electrochemical microscopy to quantify the O2 gradients present above a Pseudomonas aeruginosa biofilm. These results reveal that a biofilm produces a hypoxic zone that extends hundreds of microns from the biofilm surface within minutes and that the biofilm consumes O2 at a maximum rate. Treating the biofilm with levels of the antibiotic ciprofloxacin that kill 99% of the bacteria did not affect the O2 gradient, indicating that the biofilm is highly resilient to antimicrobial treatment in regard to O2 consumption.
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Khosravi Y, Kandukuri RDP, Palmer SR, Gloag ES, Borisov SM, Starke EM, Ward MT, Kumar P, de Beer D, Chennu A, Stoodley P. Use of an oxygen planar optode to assess the effect of high velocity microsprays on oxygen penetration in a human dental biofilms in-vitro. BMC Oral Health 2020; 20:230. [PMID: 32825831 PMCID: PMC7441732 DOI: 10.1186/s12903-020-01217-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 08/12/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Dental plaque biofilms are the causative agents of caries, gingivitis and periodontitis. Both mechanical and chemical strategies are used in routine oral hygiene strategies to reduce plaque build-up. If allowed to mature biofilms can create anoxic microenvironments leading to communities which harbor pathogenic Gram-negative anaerobes. When subjected to high velocity fluid jets and sprays biofilms can be fluidized which disrupts the biofilm structure and allows the more efficient delivery of antimicrobial agents. METHODS To investigate how such jets may disrupt anoxic niches in the biofilm, we used planar optodes to measure the dissolved oxygen (DO) concentration at the base of in-vitro biofilms grown from human saliva and dental plaque. These biofilms were subject to "shooting" treatments with a commercial high velocity microspray (HVM) device. RESULTS HVM treatment resulted in removal of much of the biofilm and a concurrent rapid shift from anoxic to oxic conditions at the base of the surrounding biofilm. We also assessed the impact of HVM treatment on the microbial community by tracking 7 target species by qPCR. There was a general reduction in copy numbers of the universal 16S RNA by approximately 95%, and changes of individual species in the target region ranged from approximately 1 to 4 log reductions. CONCLUSION We concluded that high velocity microsprays removed a sufficient amount of biofilm to disrupt the anoxic region at the biofilm-surface interface.
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Affiliation(s)
- Yalda Khosravi
- Department of Microbial Infection and Immunity, Ohio State University, Columbus, USA
| | | | - Sara R Palmer
- College of Dentistry, The Ohio State University, Columbus, OH, USA
| | - Erin S Gloag
- Department of Microbial Infection and Immunity, Ohio State University, Columbus, USA
| | - Sergey M Borisov
- Institute of Analytical Chemistry and Food Chemistry Graz University of Technology Stremayrgasse, Graz, Austria
| | | | - Marilyn T Ward
- Philips Oral Healthcare, Bothell, Washington, 98021, USA
| | - Purnima Kumar
- College of Dentistry, The Ohio State University, Columbus, OH, USA
| | - Dirk de Beer
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Arjun Chennu
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Paul Stoodley
- Department of Microbial Infection and Immunity, Ohio State University, Columbus, USA. .,Department Orthopaedics, Ohio State University, Columbus, USA. .,National Centre for Advanced Tribology (nCATS), Mechanical Engineering, University of Southampton, Southampton, UK.
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7
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Luminescent Nanosensors for Ratiometric Monitoring of Three-Dimensional Oxygen Gradients in Laboratory and Clinical Pseudomonas aeruginosa Biofilms. Appl Environ Microbiol 2019; 85:AEM.01116-19. [PMID: 31420335 DOI: 10.1128/aem.01116-19] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 08/09/2019] [Indexed: 01/08/2023] Open
Abstract
Bacterial biofilms can form persistent infections on wounds and implanted medical devices and are associated with many chronic diseases, such as cystic fibrosis. These infections are medically difficult to treat, as biofilms are more resistant to antibiotic attack than their planktonic counterparts. An understanding of the spatial and temporal variation in the metabolism of biofilms is a critical component toward improved biofilm treatments. To this end, we developed oxygen-sensitive luminescent nanosensors to measure three-dimensional (3D) oxygen gradients, an application of which is demonstrated here with Pseudomonas aeruginosa biofilms. The method was applied here and improves on traditional one-dimensional (1D) methods of measuring oxygen profiles by investigating the spatial and temporal variation of oxygen concentration when biofilms are challenged with antibiotic attack. We observed an increased oxygenation of biofilms that was consistent with cell death from comparisons with antibiotic kill curves for PAO1. Due to the spatial and temporal nature of our approach, we also identified spatial and temporal inhomogeneities in the biofilm metabolism that are consistent with previous observations. Clinical strains of P. aeruginosa subjected to similar interrogation showed variations in resistance to colistin and tobramycin, which are two antibiotics commonly used to treat P. aeruginosa infections in cystic fibrosis patients.IMPORTANCE Biofilm infections are more difficult to treat than planktonic infections for a variety of reasons, such as decreased antibiotic penetration. Their complex structure makes biofilms challenging to study without disruption. To address this limitation, we developed and demonstrated oxygen-sensitive luminescent nanosensors that can be incorporated into biofilms for studying oxygen penetration, distribution, and antibiotic efficacy-demonstrated here with our sensors monitoring antibiotic impacts on metabolism in biofilms formed from clinical isolates. The significance of our research is in demonstrating not only a nondisruptive method for imaging and measuring oxygen in biofilms but also that this nanoparticle-based sensing platform can be modified to measure many different ions and small molecule analytes.
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8
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Moßhammer M, Brodersen KE, Kühl M, Koren K. Nanoparticle- and microparticle-based luminescence imaging of chemical species and temperature in aquatic systems: a review. Mikrochim Acta 2019; 186:126. [PMID: 30680465 DOI: 10.1007/s00604-018-3202-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 12/20/2018] [Indexed: 11/25/2022]
Abstract
Most aquatic systems rely on a multitude of biogeochemical processes that are coupled with each other in a complex and dynamic manner. To understand such processes, minimally invasive analytical tools are required that allow continuous, real-time measurements of individual reactions in these complex systems. Optical chemical sensors can be used in the form of fiber-optic sensors, planar sensors, or as micro- and nanoparticles (MPs and NPs). All have their specific merits, but only the latter allow for visualization and quantification of chemical gradients over 3D structures. This review (with 147 references) summarizes recent developments mainly in the field of optical NP sensors relevant for chemical imaging in aquatic science. The review encompasses methods for signal read-out and imaging, preparation of NPs and MPs, and an overview of relevant MP/NP-based sensors. Additionally, examples of MP/NP-based sensors in aquatic systems such as corals, plant tissue, biofilms, sediments and water-sediment interfaces, marine snow and in 3D bioprinting are given. We also address current challenges and future perspectives of NP-based sensing in aquatic systems in a concluding section. Graphical abstract ᅟ.
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Affiliation(s)
- Maria Moßhammer
- Marine Biological Section, Department of Biology, University of Copenhagen, 3000, Helsingør, Denmark
| | - Kasper Elgetti Brodersen
- Marine Biological Section, Department of Biology, University of Copenhagen, 3000, Helsingør, Denmark
| | - Michael Kühl
- Marine Biological Section, Department of Biology, University of Copenhagen, 3000, Helsingør, Denmark.
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, 2007, Australia.
| | - Klaus Koren
- Aarhus University Center for Water Technology, Department of Bioscience - Microbiology, Aarhus University, 8000, Aarhus, Denmark.
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9
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Sønderholm M, Koren K, Wangpraseurt D, Jensen PØ, Kolpen M, Kragh KN, Bjarnsholt T, Kühl M. Tools for studying growth patterns and chemical dynamics of aggregated Pseudomonas aeruginosa exposed to different electron acceptors in an alginate bead model. NPJ Biofilms Microbiomes 2018; 4:3. [PMID: 29479470 PMCID: PMC5818519 DOI: 10.1038/s41522-018-0047-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 01/07/2018] [Accepted: 01/24/2018] [Indexed: 12/31/2022] Open
Abstract
In chronic infections, bacterial pathogens typically grow as small dense cell aggregates embedded in a matrix consisting of, e.g., wound bed sludge or lung mucus. Such biofilm growth mode exhibits extreme tolerance towards antibiotics and the immune defence system. The bacterial aggregates are exposed to physiological heterogeneity and O2 limitation due to steep chemical gradients through the matrix, which is are hypothesised to contribute to antibiotic tolerance. Using a novel combination of microsensor and bioimaging analysis, we investigated growth patterns and chemical dynamics of the pathogen Pseudomonas aeruginosa in an alginate bead model, which mimics growth in chronic infections better than traditional biofilm experiments in flow chambers. Growth patterns were strongly affected by electron acceptor availability and the presence of chemical gradients, where the combined presence of O2 and nitrate yielded highest bacterial growth by combined aerobic respiration and denitrification.
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Affiliation(s)
- Majken Sønderholm
- Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen N, Denmark
| | - Klaus Koren
- Marine Biology Section, Department of Biology, University of Copenhagen, Strandpromenaden 5, DK-3000 Helsingør, Denmark
| | - Daniel Wangpraseurt
- Marine Biology Section, Department of Biology, University of Copenhagen, Strandpromenaden 5, DK-3000 Helsingør, Denmark
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW UK
| | - Peter Østrup Jensen
- Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen N, Denmark
- Department of Clinical Microbiology 9301, Copenhagen University Hospital, Rigshospitalet, Juliane Maries Vej 22, Copenhagen, Denmark
| | - Mette Kolpen
- Department of Clinical Microbiology 9301, Copenhagen University Hospital, Rigshospitalet, Juliane Maries Vej 22, Copenhagen, Denmark
| | - Kasper Nørskov Kragh
- Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen N, Denmark
| | - Thomas Bjarnsholt
- Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen N, Denmark
- Department of Clinical Microbiology 9301, Copenhagen University Hospital, Rigshospitalet, Juliane Maries Vej 22, Copenhagen, Denmark
| | - Michael Kühl
- Marine Biology Section, Department of Biology, University of Copenhagen, Strandpromenaden 5, DK-3000 Helsingør, Denmark
- Climate Change Cluster, University of Technology Sydney, Broadway, NSW 2007 Australia
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10
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Rubol S, Freixa A, Sanchez-Vila X, Romaní AM. Linking biofilm spatial structure to real-time microscopic oxygen decay imaging. BIOFOULING 2018; 34:200-211. [PMID: 29405091 DOI: 10.1080/08927014.2017.1423474] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2017] [Accepted: 12/28/2017] [Indexed: 06/07/2023]
Abstract
Two non-destructive techniques, confocal laser scanning microscopy (CLSM) and planar optode (VisiSens imaging), were combined to relate the fine-scale spatial structure of biofilm components to real-time images of oxygen decay in aquatic biofilms. Both techniques were applied to biofilms grown for seven days at contrasting light and temperature (10/20°C) conditions. The geo-statistical analyses of CLSM images indicated that biofilm structures consisted of small (~100 μm) and middle sized (~101 μm) irregular aggregates. Cyanobacteria and EPS (extracellular polymeric substances) showed larger aggregate sizes in dark grown biofilms while, for algae, aggregates were larger in light-20°C conditions. Light-20°C biofilms were most dense while 10°C biofilms showed a sparser structure and lower respiration rates. There was a positive relationship between the number of pixels occupied and the oxygen decay rate. The combination of optodes and CLMS, taking advantage of geo-statistics, is a promising way to relate biofilm architecture and metabolism at the micrometric scale.
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Affiliation(s)
- S Rubol
- a Department of Energy Resources Engineering , Stanford University , Stanford , CA , USA
| | - A Freixa
- b Catalan Institute for Water Research (ICRA) , Girona , Spain
| | - X Sanchez-Vila
- c Hydrogeology Group, Department of Civil and Environmental Engineering , Universitat Politècnica de Catalunya, UPC , Barcelona , Spain
| | - A M Romaní
- d Institute of Aquatic Ecology , University of Girona , Girona , Spain
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Sarafbidabad M, Parsaee Z, Noor Mohammadi Z, Karachi N, Razavi R. Novel double layer film composed of reduced graphene oxide and Rose Bengal dye: design, fabrication and evaluation as an efficient chemosensor for silver(i) detection. NEW J CHEM 2018. [DOI: 10.1039/c8nj01796d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A novel silver-chemosensor fabricated with reduced graphene oxide and Rose Bengal (RB) based on the interaction of Ag+ and RB.
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Affiliation(s)
- Mohsen Sarafbidabad
- Department of Biomedical Engineering
- Faculty of Engineering
- University of Isfahan
- Isfahan
- Iran
| | - Zohreh Parsaee
- Young Researchers and Elite Club
- Bushehr Branch
- Islamic Azad University
- Bushehr
- Iran
| | - Zahra Noor Mohammadi
- Department of Chemistry
- Khozestan Science and Research Branch
- Islamic Azad University
- Khozestan
- Iran
| | - Nima Karachi
- Department of Chemistry
- Islamic Azad University
- Marvdasht
- Iran
| | - Razieh Razavi
- Department of Chemistry
- Faculty of Science
- University of Jiroft
- Jiroft
- Iran
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12
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Martirani-Von Abercron SM, Marín P, Solsona-Ferraz M, Castañeda-Cataña MA, Marqués S. Naphthalene biodegradation under oxygen-limiting conditions: community dynamics and the relevance of biofilm-forming capacity. Microb Biotechnol 2017; 10:1781-1796. [PMID: 28840968 PMCID: PMC5658598 DOI: 10.1111/1751-7915.12842] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 07/21/2017] [Accepted: 07/25/2017] [Indexed: 11/27/2022] Open
Abstract
Toxic polycyclic aromatic hydrocarbons (PAHs) are frequently released into the environment from anthropogenic sources. PAH remediation strategies focus on biological processes mediated by bacteria. The availability of oxygen in polluted environments is often limited or absent, and only bacteria able to thrive in these conditions can be considered for bioremediation strategies. To identify bacterial strains able to degrade PAHs under oxygen‐limiting conditions, we set up enrichment cultures from samples of an oil‐polluted aquifer, using either anoxic or microaerophilic condition and with PAHs as the sole carbon source. Despite the presence of a significant community of nitrate‐reducing bacteria, the initial community, which was dominated by Betaproteobacteria, was incapable of PAH degradation under strict anoxic conditions, although a clear shift in the structure of the community towards an increase in the Alphaproteobacteria (Sphingomonadaceae), Actinobacteria and an uncultured group of Acidobacteria was observed in the enrichments. In contrast, growth under microaerophilic conditions with naphthalene as the carbon source evidenced the development of a biofilm structure around the naphthalene crystal. The enrichment process selected two co‐dominant groups which finally reached 97% of the bacterial communities: Variovorax spp. (54%, Betaproteobacteria) and Starkeya spp. (43%, Xanthobacteraceae). The two dominant populations were able to grow with naphthalene, although only Starkeya was able to reproduce the biofilm structure around the naphthalene crystal. The pathway for naphthalene degradation was identified, which included as essential steps dioxygenases with high affinity for oxygen, showing 99% identity with Xanthobacter polyaromaticivorans dbd cluster for PAH degradation. Our results suggest that the biofilm formation capacity of Starkeya provided a structure to allocate its cells at an appropriate distance from the toxic carbon source.
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Affiliation(s)
| | - Patricia Marín
- Estación Experimental del Zaidín, Department of Environmental Protection, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Marta Solsona-Ferraz
- Estación Experimental del Zaidín, Department of Environmental Protection, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Mayra-Alejandra Castañeda-Cataña
- Estación Experimental del Zaidín, Department of Environmental Protection, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Silvia Marqués
- Estación Experimental del Zaidín, Department of Environmental Protection, Consejo Superior de Investigaciones Científicas, Granada, Spain
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13
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Jensen PØ, Kolpen M, Kragh KN, Kühl M. Microenvironmental characteristics and physiology of biofilms in chronic infections of CF patients are strongly affected by the host immune response. APMIS 2017; 125:276-288. [PMID: 28407427 DOI: 10.1111/apm.12668] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Accepted: 01/04/2017] [Indexed: 01/14/2023]
Abstract
In vitro studies of Pseudomonas aeruginosa and other pathogenic bacteria in biofilm aggregates have yielded detailed insight into their potential growth modes and metabolic flexibility under exposure to gradients of substrate and electron acceptor. However, the growth pattern of P. aeruginosa in chronic lung infections of cystic fibrosis (CF) patients is very different from what is observed in vitro, for example, in biofilms grown in flow chambers. Dense in vitro biofilms of P. aeruginosa exhibit rapid O2 depletion within <50-100 μm due to their own aerobic metabolism. In contrast, in vivo investigations show that P. aeruginosa persists in the chronically infected CF lung as relatively small cell aggregates that are surrounded by numerous PMNs, where the activity of PMNs is the major cause of O2 depletion rendering the P. aeruginosa aggregates anoxic. High levels of nitrate and nitrite enable P. aeruginosa to persist fueled by denitrification in the PMN-surrounded biofilm aggregates. This configuration creates a potentially long-term stable ecological niche for P. aeruginosa in the CF lung, which is largely governed by slow growth and anaerobic metabolism and enables persistence and resilience of this pathogen even under the recurring aggressive antimicrobial treatments of CF patients. As similar slow growth of other CF pathogens has recently been observed in endobronchial secretions, there is now a clear need for better in vitro models that simulate such in vivo growth patterns and anoxic microenvironments in order to help unravel the efficiency of existing or new antimicrobials targeting anaerobic metabolism in P. aeruginosa and other CF pathogens. We also advocate that host immune responses such as PMN-driven O2 depletion play a central role in the formation of anoxic microniches governing bacterial persistence in other chronic infections such as chronic wounds.
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Affiliation(s)
- Peter Ø Jensen
- Department of Clinical Microbiology, Rigshospitalet, Copenhagen, Denmark.,Department of International Health, Immunology and Microbiology, UC-CARE, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Mette Kolpen
- Department of Clinical Microbiology, Rigshospitalet, Copenhagen, Denmark.,Department of International Health, Immunology and Microbiology, UC-CARE, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Kasper N Kragh
- Department of Clinical Microbiology, Rigshospitalet, Copenhagen, Denmark.,Department of International Health, Immunology and Microbiology, UC-CARE, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Michael Kühl
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark.,Climate Change Cluster, University of Technology, Sydney, NSW, Australia
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14
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Wagner M, Horn H. Optical coherence tomography in biofilm research: A comprehensive review. Biotechnol Bioeng 2017; 114:1386-1402. [DOI: 10.1002/bit.26283] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 02/10/2017] [Accepted: 03/01/2017] [Indexed: 01/29/2023]
Affiliation(s)
- Michael Wagner
- Karlsruhe Institute of Technology; Engler-Bunte-Institut; Chair of Water Chemistry and Water Technology; Engler-Bunte-Ring 9 76131 Karlsruhe Germany
- Karlsruhe Institute of Technology; Institute of Functional Interfaces; Eggenstein-Leopoldshafen Germany
| | - Harald Horn
- Karlsruhe Institute of Technology; Engler-Bunte-Institut; Chair of Water Chemistry and Water Technology; Engler-Bunte-Ring 9 76131 Karlsruhe Germany
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15
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Spatial heterogeneity of biofouling under different cross-flow velocities in reverse osmosis membrane systems. J Memb Sci 2016. [DOI: 10.1016/j.memsci.2016.08.065] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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16
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Zou X, Pan T, Chen L, Tian Y, Zhang W. Luminescence materials for pH and oxygen sensing in microbial cells - structures, optical properties, and biological applications. Crit Rev Biotechnol 2016; 37:723-738. [PMID: 27627832 DOI: 10.1080/07388551.2016.1223011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Luminescence including fluorescence and phosphorescence sensors have been demonstrated to be important for studying cell metabolism, and diagnosing diseases and cancer. Various design principles have been employed for the development of sensors in different formats, such as organic molecules, polymers, polymeric hydrogels, and nanoparticles. The integration of the sensing with fluorescence imaging provides valuable tools for biomedical research and applications at not only bulk-cell level but also at single-cell level. In this article, we critically reviewed recent progresses on pH, oxygen, and dual pH and oxygen sensors specifically for their application in microbial cells. In addition, we focused not only on sensor materials with different chemical structures, but also on design and applications of sensors for better understanding cellular metabolism of microbial cells. Finally, we also provided an outlook for future materials design and key challenges in reaching broad applications in microbial cells.
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Affiliation(s)
- Xianshao Zou
- a Department of Materials Science and Engineering , South University of Science and Technology of China , Shenzhen , Guangdong , P.R. China
| | - Tingting Pan
- a Department of Materials Science and Engineering , South University of Science and Technology of China , Shenzhen , Guangdong , P.R. China
| | - Lei Chen
- b Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology , Tianjin University , Tianjin , P.R. China.,c Key Laboratory of Systems Bioengineering, Ministry of Education of China , Tianjin , P.R. China.,d SynBio Platform, Collaborative Innovation Center of Chemical Science and Engineering , Tianjin , P.R. China
| | - Yanqing Tian
- a Department of Materials Science and Engineering , South University of Science and Technology of China , Shenzhen , Guangdong , P.R. China
| | - Weiwen Zhang
- b Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology , Tianjin University , Tianjin , P.R. China.,c Key Laboratory of Systems Bioengineering, Ministry of Education of China , Tianjin , P.R. China.,d SynBio Platform, Collaborative Innovation Center of Chemical Science and Engineering , Tianjin , P.R. China
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17
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Micro- and nanostructured sol-gel-based materials for optical chemical sensing (2005–2015). Mikrochim Acta 2016. [DOI: 10.1007/s00604-016-1863-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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18
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Moßhammer M, Strobl M, Kühl M, Klimant I, Borisov SM, Koren K. Design and Application of an Optical Sensor for Simultaneous Imaging of pH and Dissolved O2 with Low Cross-Talk. ACS Sens 2016. [DOI: 10.1021/acssensors.6b00071] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Maria Moßhammer
- Marine
Biological Section, Department of Biology, University of Copenhagen, 3000 Helsingør, Denmark
- Institute
of Analytical Chemistry and Food Chemistry, Graz University of Technology, 8010 Graz, Austria
| | - Martin Strobl
- Institute
of Analytical Chemistry and Food Chemistry, Graz University of Technology, 8010 Graz, Austria
| | - Michael Kühl
- Marine
Biological Section, Department of Biology, University of Copenhagen, 3000 Helsingør, Denmark
- Plant
Functional Biology and Climate Change Cluster, University of Technology Sydney, Ultimo, New South Wales 2007, Australia
| | - Ingo Klimant
- Institute
of Analytical Chemistry and Food Chemistry, Graz University of Technology, 8010 Graz, Austria
| | - Sergey M. Borisov
- Institute
of Analytical Chemistry and Food Chemistry, Graz University of Technology, 8010 Graz, Austria
| | - Klaus Koren
- Marine
Biological Section, Department of Biology, University of Copenhagen, 3000 Helsingør, Denmark
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19
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Gashti MP, Asselin J, Barbeau J, Boudreau D, Greener J. A microfluidic platform with pH imaging for chemical and hydrodynamic stimulation of intact oral biofilms. LAB ON A CHIP 2016; 16:1412-9. [PMID: 26956837 DOI: 10.1039/c5lc01540e] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
A microfluidic platform with a fluorescent nanoparticle-based sensor is demonstrated for real-time, ratiometric pH imaging of biofilms. Sensing is accomplished by a thin patterned layer of covalently bonded Ag@SiO2+FiTC nanoparticles on an embedded planar glass substrate. The system is designed to be sensitive, responsive and give sufficient spatial resolution to enable new micro-scale studies of the dynamic response of oral biofilms to well-controlled chemical and hydrodynamic stimulation. Performance under challenging operational conditions is demonstrated, which include long-duration exposure to sheer stresses, photoexcitation and pH sensor biofouling. After comprehensive validation, the device was used to monitor pH changes at the attachment surface of a biofilm of the oral bacteria, Streptococcus salivarius. By controlling flow and chemical concentration conditions in the microchannel, biochemical and mass transport contributions to the Stephan curve could be probed individually. This opens the way for the analysis of separate contributions to dental caries due to localized acidification directly at the biofilm tooth interface.
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Affiliation(s)
| | - J Asselin
- Département de chimie, Université Laval, Québec (QC), G1V 0A6 Canada. and Centre d'optique, photonique et laser (COPL), Québec (QC), G1V 0A6 Canada
| | - J Barbeau
- Faculté de médecine dentaire, Université de Montréal (QC), H3C 3J4 Canada
| | - D Boudreau
- Département de chimie, Université Laval, Québec (QC), G1V 0A6 Canada. and Centre d'optique, photonique et laser (COPL), Québec (QC), G1V 0A6 Canada
| | - J Greener
- Département de chimie, Université Laval, Québec (QC), G1V 0A6 Canada.
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20
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Farhat NM, Staal M, Siddiqui A, Borisov SM, Bucs SS, Vrouwenvelder JS. Early non-destructive biofouling detection and spatial distribution: Application of oxygen sensing optodes. WATER RESEARCH 2015; 83:10-20. [PMID: 26117369 DOI: 10.1016/j.watres.2015.06.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 06/07/2015] [Accepted: 06/09/2015] [Indexed: 06/04/2023]
Abstract
Biofouling is a serious problem in reverse osmosis/nanofiltration (RO/NF) applications, reducing membrane performance. Early detection of biofouling plays an essential role in an adequate anti-biofouling strategy. Presently, fouling of membrane filtration systems is mainly determined by measuring changes in pressure drop, which is not exclusively linked to biofouling. Non-destructive imaging of oxygen concentrations (i) is specific for biological activity of biofilms and (ii) may enable earlier detection of biofilm accumulation than pressure drop. The objective of this study was to test whether transparent luminescent planar O2 optodes, in combination with a simple imaging system, can be used for early non-destructive biofouling detection. This biofouling detection is done by mapping the two-dimensional distribution of O2 concentrations and O2 decrease rates inside a membrane fouling simulator (MFS). Results show that at an early stage, biofouling development was detected by the oxygen sensing optodes while no significant increase in pressure drop was yet observed. Additionally, optodes could detect spatial heterogeneities in biofouling distribution at a micro scale. Biofilm development started mainly at the feed spacer crossings. The spatial and quantitative information on biological activity will lead to better understanding of the biofouling processes, contributing to the development of more effective biofouling control strategies.
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Affiliation(s)
- N M Farhat
- Water Desalination and Reuse Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia.
| | - M Staal
- Water Desalination and Reuse Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - A Siddiqui
- Water Desalination and Reuse Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - S M Borisov
- Graz University of Technology, Institute of Analytical Chemistry and Food Chemistry, Stremayrgasse 9, 8010 Graz, Austria
| | - Sz S Bucs
- Water Desalination and Reuse Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - J S Vrouwenvelder
- Water Desalination and Reuse Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia; Delft University of Technology, Faculty of Applied Sciences, Department of Biotechnology, Julianalaan 67, 2628 BC Delft, The Netherlands; Wetsus, European Centre of Excellence for Sustainable Water Technology, Oostergoweg 9, 8911 MA Leeuwarden, The Netherlands
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21
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Aristotelous AC, Klapper I, Grabovsky Y, Pabst B, Pitts B, Stewart PS. Diffusive transport through a model host-biofilm system. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015; 92:022703. [PMID: 26382428 PMCID: PMC6192257 DOI: 10.1103/physreve.92.022703] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Indexed: 06/05/2023]
Abstract
Free-living biofilms have been subject to considerable attention, and basic physical principles for them are generally accepted. Many host-biofilm systems, however, consist of heterogeneous mixtures of aggregates of microbes intermixed with host material and are much less studied. Here we analyze a key property, namely reactive depletion, in such systems and argue that two regimes are possible: (1) a homogenizable mixture of biofilm and host that in important ways acts effectively like a homogeneous macrobiofilm and (2) a distribution of separated microbiofilms within the host with independent local microenvironments.
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Affiliation(s)
- A C Aristotelous
- Department of Mathematics, Temple University, Philadelphia, Pennsylvania, USA
| | - I Klapper
- Department of Mathematics, Temple University, Philadelphia, Pennsylvania, USA
- Center for Biofilm Engineering, Montana State University, Bozeman, Montana, USA
| | - Y Grabovsky
- Department of Mathematics, Temple University, Philadelphia, Pennsylvania, USA
| | - B Pabst
- Center for Biofilm Engineering, Montana State University, Bozeman, Montana, USA
| | - B Pitts
- Center for Biofilm Engineering, Montana State University, Bozeman, Montana, USA
| | - P S Stewart
- Center for Biofilm Engineering, Montana State University, Bozeman, Montana, USA
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22
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Mikhelson KN, Peshkova MA. Advances and trends in ionophore-based chemical sensors. RUSSIAN CHEMICAL REVIEWS 2015. [DOI: 10.1070/rcr4506] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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23
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Santner J, Larsen M, Kreuzeder A, Glud RN. Two decades of chemical imaging of solutes in sediments and soils--a review. Anal Chim Acta 2015; 878:9-42. [PMID: 26002324 DOI: 10.1016/j.aca.2015.02.006] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Revised: 02/03/2015] [Accepted: 02/05/2015] [Indexed: 01/08/2023]
Abstract
The increasing appreciation of the small-scale (sub-mm) heterogeneity of biogeochemical processes in sediments, wetlands and soils has led to the development of several methods for high-resolution two-dimensional imaging of solute distribution in porewaters. Over the past decades, localised sampling of solutes (diffusive equilibration in thin films, diffusive gradients in thin films) followed by planar luminescent sensors (planar optodes) have been used as analytical tools for studies on solute distribution and dynamics. These approaches have provided new conceptual and quantitative understanding of biogeochemical processes regulating the distribution of key elements and solutes including O2, CO2, pH, redox conditions as well as nutrient and contaminant ion species in structurally complex soils and sediments. Recently these methods have been applied in parallel or integrated as so-called sandwich sensors for multianalyte measurements. Here we review the capabilities and limitations of the chemical imaging methods that are currently at hand, using a number of case studies, and provide an outlook on potential future developments for two-dimensional solute imaging in soils and sediments.
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Affiliation(s)
- Jakob Santner
- Rhizosphere Ecology and Biogeochemistry Group, Department of Forest and Soil Sciences, Institute of Soil Research, University of Natural Resources and Life Sciences Vienna, Konrad Lorenz-Strasse 24, 3430 Tulln, Austria.
| | - Morten Larsen
- Nordic Center for Earth Evolution (NordCEE), University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark
| | - Andreas Kreuzeder
- Rhizosphere Ecology and Biogeochemistry Group, Department of Forest and Soil Sciences, Institute of Soil Research, University of Natural Resources and Life Sciences Vienna, Konrad Lorenz-Strasse 24, 3430 Tulln, Austria
| | - Ronnie N Glud
- Nordic Center for Earth Evolution (NordCEE), University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark; Scottish Marine Institute, Scottish Association for Marine Science, Oban, Scotland, PA37 1QA, UK; Greenland Climate Research Centre (CO Greenland Institute of Natural Resources), Kivioq 2, Box 570, 3900 Nuuk, Greenland; Arctic Research Centre, Aarhus University, 8000 Aarhus, Denmark
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24
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Billings N, Birjiniuk A, Samad TS, Doyle PS, Ribbeck K. Material properties of biofilms-a review of methods for understanding permeability and mechanics. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2015; 78:036601. [PMID: 25719969 PMCID: PMC4504244 DOI: 10.1088/0034-4885/78/3/036601] [Citation(s) in RCA: 110] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Microorganisms can form biofilms, which are multicellular communities surrounded by a hydrated extracellular matrix of polymers. Central properties of the biofilm are governed by this extracellular matrix, which provides mechanical stability to the 3D biofilm structure, regulates the ability of the biofilm to adhere to surfaces, and determines the ability of the biofilm to adsorb gases, solutes, and foreign cells. Despite their critical relevance for understanding and eliminating of biofilms, the materials properties of the extracellular matrix are understudied. Here, we offer the reader a guide to current technologies that can be utilized to specifically assess the permeability and mechanical properties of the biofilm matrix and its interacting components. In particular, we highlight technological advances in instrumentation and interactions between multiple disciplines that have broadened the spectrum of methods available to conduct these studies. We review pioneering work that furthers our understanding of the material properties of biofilms.
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Affiliation(s)
- Nicole Billings
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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25
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Abstract
Cells within biofilms exhibit physiological heterogeneity, in part because of chemical gradients existing within these spatially structured communities. Previous work has examined how chemical gradients develop in large biofilms containing >108 cells. However, many bacterial communities in nature are composed of small, densely packed aggregates of cells (≤105 bacteria). Using a gelatin-based three-dimensional (3D) printing strategy, we confined the bacterium Pseudomonas aeruginosa within picoliter-sized 3D “microtraps” that are permeable to nutrients, waste products, and other bioactive small molecules. We show that as a single bacterium grows into a maximally dense (1012 cells ml−1) clonal population, a localized depletion of oxygen develops when it reaches a critical aggregate size of ~55 pl. Collectively, these data demonstrate that chemical and phenotypic heterogeneity exists on the micrometer scale within small aggregate populations. Before developing into large, complex communities, microbes initially cluster into aggregates, and it is unclear if chemical heterogeneity exists in these ubiquitous micrometer-scale aggregates. We chose to examine oxygen availability within an aggregate since oxygen concentration impacts a number of important bacterial processes, including metabolism, social behaviors, virulence, and antibiotic resistance. By determining that oxygen availability can vary within aggregates containing ≤105 bacteria, we establish that physiological heterogeneity exists within P. aeruginosa aggregates, suggesting that such heterogeneity frequently exists in many naturally occurring small populations.
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26
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Schutting S, Klimant I, de Beer D, Borisov SM. New highly fluorescent pH indicator for ratiometric RGB imaging of pCO2. Methods Appl Fluoresc 2014; 2:024001. [DOI: 10.1088/2050-6120/2/2/024001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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27
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Kim CK, Duong HD, Rhee JI. Preparation of an optical sensing membrane for triple detection of oxygen, pH, and temperature using response surface methodology. Microchem J 2013. [DOI: 10.1016/j.microc.2013.08.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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28
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Bjarnsholt T, Alhede M, Alhede M, Eickhardt-Sørensen SR, Moser C, Kühl M, Jensen PØ, Høiby N. The in vivo biofilm. Trends Microbiol 2013; 21:466-74. [PMID: 23827084 DOI: 10.1016/j.tim.2013.06.002] [Citation(s) in RCA: 498] [Impact Index Per Article: 45.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Revised: 05/26/2013] [Accepted: 06/05/2013] [Indexed: 11/15/2022]
Abstract
Bacteria can grow and proliferate either as single, independent cells or organized in aggregates commonly referred to as biofilms. When bacteria succeed in forming a biofilm within the human host, the infection often becomes very resistant to treatment and can develop into a chronic state. Biofilms have been studied for decades using various in vitro models, but it remains debatable whether such in vitro biofilms actually resemble in vivo biofilms in chronic infections. In vivo biofilms share several structural characteristics that differ from most in vitro biofilms. Additionally, the in vivo experimental time span and presence of host defenses differ from chronic infections and the chemical microenvironment of both in vivo and in vitro biofilms is seldom taken into account. In this review, we discuss why the current in vitro models of biofilms might be limited for describing infectious biofilms, and we suggest new strategies for improving this discrepancy.
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Affiliation(s)
- Thomas Bjarnsholt
- Department of International Health, Immunology, and Microbiology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark; Department of Clinical Microbiology 9301, Juliane Mariesvej 22, Copenhagen University Hospital, Copenhagen, Denmark.
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29
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Kühl M, Behrendt L, Trampe E, Qvortrup K, Schreiber U, Borisov SM, Klimant I, Larkum AWD. Microenvironmental Ecology of the Chlorophyll b-Containing Symbiotic Cyanobacterium Prochloron in the Didemnid Ascidian Lissoclinum patella. Front Microbiol 2012; 3:402. [PMID: 23226144 PMCID: PMC3510431 DOI: 10.3389/fmicb.2012.00402] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Accepted: 11/02/2012] [Indexed: 11/13/2022] Open
Abstract
The discovery of the cyanobacterium Prochloron was the first finding of a bacterial oxyphototroph with chlorophyll (Chl) b, in addition to Chl a. It was first described as Prochloron didemni but a number of clades have since been described. Prochloron is a conspicuously large (7-25 μm) unicellular cyanobacterium living in a symbiotic relationship, primarily with (sub-) tropical didemnid ascidians; it has resisted numerous cultivation attempts and appears truly obligatory symbiotic. Recently, a Prochloron draft genome was published, revealing no lack of metabolic genes that could explain the apparent inability to reproduce and sustain photosynthesis in a free-living stage. Possibly, the unsuccessful cultivation is partly due to a lack of knowledge about the microenvironmental conditions and ecophysiology of Prochloron in its natural habitat. We used microsensors, variable chlorophyll fluorescence imaging and imaging of O(2) and pH to obtain a detailed insight to the microenvironmental ecology and photobiology of Prochloron in hospite in the didemnid ascidian Lissoclinum patella. The microenvironment within ascidians is characterized by steep gradients of light and chemical parameters that change rapidly with varying irradiances. The interior zone of the ascidians harboring Prochloron thus became anoxic and acidic within a few minutes of darkness, while the same zone exhibited O(2) super-saturation and strongly alkaline pH after a few minutes of illumination. Photosynthesis showed lack of photoinhibition even at high irradiances equivalent to full sunlight, and photosynthesis recovered rapidly after periods of anoxia. We discuss these new insights on the ecological niche of Prochloron and possible interactions with its host and other microbes in light of its recently published genome and a recent study of the overall microbial diversity and metagenome of L. patella.
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Affiliation(s)
- Michael Kühl
- Marine Biological Section, Department of Biology, University of CopenhagenHelsingør, Denmark
- Plant Functional Biology and Climate Change Cluster, University of Technology SydneySydney, NSW, Australia
- Singapore Centre on Environmental Life Sciences Engineering, School of Biological Sciences, Nanyang Technological UniversitySingapore
| | - Lars Behrendt
- Marine Biological Section, Department of Biology, University of CopenhagenHelsingør, Denmark
| | - Erik Trampe
- Marine Biological Section, Department of Biology, University of CopenhagenHelsingør, Denmark
| | - Klaus Qvortrup
- Department of Biomedical Sciences, Core Facility for Integrated Microscopy, University of CopenhagenCopenhagen, Denmark
| | - Ulrich Schreiber
- Julius-von-Sachs Institut für Biowissenschaften, Universität WürzburgWürzburg, Germany
| | - Sergey M. Borisov
- Department of Analytical and Food Chemistry, Technical University of GrazGraz, Austria
| | - Ingo Klimant
- Department of Analytical and Food Chemistry, Technical University of GrazGraz, Austria
| | - Anthony W. D. Larkum
- Plant Functional Biology and Climate Change Cluster, University of Technology SydneySydney, NSW, Australia
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30
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Prest E, Staal M, Kühl M, van Loosdrecht M, Vrouwenvelder J. Quantitative measurement and visualization of biofilm O2 consumption rates in membrane filtration systems. J Memb Sci 2012. [DOI: 10.1016/j.memsci.2011.12.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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31
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Abstract
Water that flows around a biofilm influences the transport of solutes into and out of the biofilm and applies forces to the biofilm that can cause it to deform and detach. Engineering approaches to quantifying and understanding these phenomena are reviewed in the context of biofilm systems. The slow-moving fluid adjacent to the biofilm acts as an insulator for diffusive exchange. External mass transfer resistance is important because it can exacerbate oxygen or nutrient limitation in biofilms, worsen product inhibition, affect quorum sensing, and contribute to the development of tall, fingerlike biofilm clusters. Measurements of fluid motion around biofilms by particle velocimetry and magnetic resonance imaging indicate that water flows around, but not through biofilm cell clusters. Moving fluid applies forces to biofilms resulting in diverse outcomes including viscoelastic deformation, rolling, development of streamers, oscillatory movement, and material failure or detachment. The primary force applied to the biofilm is a shear force in the main direction of fluid flow, but complex hydrodynamics including eddies, vortex streets, turbulent wakes, and turbulent bursts result in additional force components.
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Affiliation(s)
- Philip S Stewart
- Center for Biofilm Engineering and Department of Chemical and Biological Engineering, Montana State University-Bozeman, Bozeman, Montana 59717-3980, USA.
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32
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Staal M, Prest EI, Vrouwenvelder JS, Rickelt LF, Kühl M. A simple optode based method for imaging O2 distribution and dynamics in tap water biofilms. WATER RESEARCH 2011; 45:5027-5037. [PMID: 21803395 DOI: 10.1016/j.watres.2011.07.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2011] [Revised: 05/25/2011] [Accepted: 07/03/2011] [Indexed: 05/31/2023]
Abstract
A ratiometric luminescence intensity imaging approach is presented, which enables spatial O2 measurements in biofilm reactors with transparent planar O2 optodes. Optodes consist of an O2 sensitive luminescent dye immobilized in a 1-10 μm thick polymeric layer on a transparent carrier, e.g. a glass window. The method is based on sequential imaging of the O2 dependent luminescence intensity, which are subsequently normalized with luminescent intensity images recorded under anoxic conditions. We present 2-dimensional O2 distribution images at the base of a tap water biofilm measured with the new ratiometric method and compare the results with O2 distribution images obtained in the same biofilm reactor with luminescence lifetime imaging. Using conventional digital cameras, such simple normalized luminescence intensity imaging can yield images of 2-dimensional O2 distributions with a high signal-to-noise ratio and spatial resolution comparable or even surpassing those obtained with expensive and complex luminescence lifetime imaging systems. The method can be applied to biofilm growth incubators allowing intermittent experimental shifts to anoxic conditions or in systems, in which the O2 concentration is depleted during incubation.
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Affiliation(s)
- M Staal
- Marine Biological Section, Department of Biology, University of Copenhagen, Strandpromenaden 5, DK-3000 Helsingør, Denmark.
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