Analysis of microbial communities with electrochemical microsensors and microscale biosensors

Enzyme-Modified Microelectrode for Simultaneous Local Measurements of O2 and pH

The use of miniaturized probes opens a new dimension in the analysis of (bio)chemical processes, enabling the possibility to perform measurements with local resolution. In addition, multiparametric measurements are highly valuable for a holistic understanding of the investigated process. Therefore, different strategies have been suggested for simultaneous local measurements of various parameters. Electroanalytical methods are a powerful strategy in this direction. However, they have been mainly restricted to coupling concurrent independent measurements with different miniaturized probes. Here, we present an enzymatic microbiosensor for the simultaneous detection of O2 and pH. The sensing strategy is based on the pH-dependent bioelectrocatalytic process associated with O2 reduction at a gold microelectrode modified with a multicopper oxidase. After initial investigations of the bioelectrocatalytic reaction over gold macroelectrodes, the fabrication and characterization of micrometer-sized probes are presented. The microbioelectrode exhibits a linear current increase with O2 concentration extending to 17.2 mg L-1, with a sensitivity of (5.56 ± 0.13) nA L mg-1 and a limit of detection of (0.5 ± 0.3) mg L-1. Moreover, a linear response allowing pH detection is obtained between pH 5.2 and 7.5 with a slope of -(47 ± 8) mV per pH unit. In addition, two proof-of-concept analytical examples are shown, demonstrating the capability of the developed sensing system for simultaneous local measurements of O2 and pH. Compared with other miniaturized probes reported before for simultaneous detection, our strategy stands out as the two investigated parameters are acquired from the very same measurement. This strategy greatly simplifies the analytical setup and for the first time provides truly simultaneous local detection in the micrometer scale.

Considerations on the use of microsensors to profile dissolved H2 concentrations in microbial electrochemical reactors

Measuring the distribution and dynamics of H2 in microbial electrochemical reactors is valuable to gain insights into the processes behind novel bioelectrochemical technologies, such as microbial electrosynthesis. Here, a microsensor method to measure and profile dissolved H2 concentrations in standard H-cell reactors is described. Graphite cathodes were oriented horizontally to enable the use of a motorized microprofiling system and a stereomicroscope was used to place the H2 microsensor precisely on the cathode surface. Profiling was performed towards the gas-liquid interface, while preserving the electric connections and flushing the headspace (to maintain anoxic conditions) and under strict temperature control (to overcome the temperature sensitivity of the microsensors). This method was tested by profiling six reactors, with and without inoculation of the acetogen Sporomusa ovata, at three different time points. H2 accumulated over time in the abiotic controls, while S. ovata maintained low H2 concentrations throughout the liquid phase (< 4 μM) during the whole experimental period. These results demonstrate that this setup generated insightful H2 profiles. However, various limitations of this microsensor method were identified, as headspace flushing lowered the dissolved H2 concentrations over time. Moreover, microsensors can likely not accurately measure H2 in the immediate vicinity of the solid cathode, because the solids cathode surface obstructs H2 diffusion into the microsensor. Finally, the reactors had to be discarded after microsensor profiling. Interested users should bear these considerations in mind when applying microsensors to characterize microbial electrochemical reactors.

How to study biofilms: technological advancements in clinical biofilm research

Biofilm formation is an important survival strategy commonly used by bacteria and fungi, which are embedded in a protective extracellular matrix of organic polymers. They are ubiquitous in nature, including humans and other animals, and they can be surface- and non-surface-associated, making them capable of growing in and on many different parts of the body. Biofilms are also complex, forming polymicrobial communities that are difficult to eradicate due to their unique growth dynamics, and clinical infections associated with biofilms are a huge burden in the healthcare setting, as they are often difficult to diagnose and to treat. Our understanding of biofilm formation and development is a fast-paced and important research focus. This review aims to describe the advancements in clinical biofilm research, including both in vitro and in vivo biofilm models, imaging techniques and techniques to analyse the biological functions of the biofilm.

Formation and emergent dynamics of spatially organized microbial systems

Spatial organization is the norm rather than the exception in the microbial world. While the study of microbial physiology has been dominated by studies in well-mixed cultures, there is now increasing interest in understanding the role of spatial organization in microbial physiology, coexistence and evolution. Where studied, spatial organization has been shown to influence all three of these aspects. In this mini review and perspective article, we emphasize that the dynamics within spatially organized microbial systems (SOMS) are governed by feedbacks between local physico-chemical conditions, cell physiology and movement, and evolution. These feedbacks can give rise to emergent dynamics, which need to be studied through a combination of spatio-temporal measurements and mathematical models. We highlight the initial formation of SOMS and their emergent dynamics as two open areas of investigation for future studies. These studies will benefit from the development of model systems that can mimic natural ones in terms of species composition and spatial structure.

Detection and Characterization of Bacterial Biofilms and Biofilm-Based Sensors

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.

Microvascular Tissue Engineering-A Review

Tissue engineering and regenerative medicine have come a long way in recent decades, but the lack of functioning vasculature is still a major obstacle preventing the development of thicker, physiologically relevant tissue constructs. A large part of this obstacle lies in the development of the vessels on a microscale-the microvasculature-that are crucial for oxygen and nutrient delivery. In this review, we present the state of the art in the field of microvascular tissue engineering and demonstrate the challenges for future research in various sections of the field. Finally, we illustrate the potential strategies for addressing some of those challenges.

Nanostructured metal oxide semiconductor-based sensors for greenhouse gas detection: progress and challenges

Climate change and global warming have been two massive concerns for the scientific community during the last few decades. Anthropogenic emissions of greenhouse gases (GHGs) have greatly amplified the level of greenhouse gases in the Earth's atmosphere which results in the gradual heating of the atmosphere. The precise measurement and reliable quantification of GHGs emission in the environment are of the utmost priority for the study of climate change. The detection of GHGs such as carbon dioxide, methane, nitrous oxide and ozone is the first and foremost step in finding the solution to manage and reduce the concentration of these gases in the Earth's atmosphere. The nanostructured metal oxide semiconductor (NMOS) based technologies for sensing GHGs emission have been found most reliable and accurate. Owing to their fascinating structural and morphological properties metal oxide semiconductors become an important class of materials for GHGs emission sensing technology. In this review article, the current concentration of GHGs in the Earth's environment, dominant sources of anthropogenic emissions of these gases and consequently their possible impacts on human life have been described briefly. Further, the different available technologies for GHG sensors along with their principle of operation have been largely discussed. The advantages and disadvantages of each sensor technology have also been highlighted. In particular, this article presents a comprehensive study on the development of various NMOS-based GHGs sensors and their performance analysis in order to establish a strong detection technology for the anthropogenic GHGs. In the last, the scope for improved sensitivity, selectivity and response time for these sensors, their future trends and outlook for researchers are suggested in the conclusion of this article.

Visualizing NH3 emission and the local O2 and pH microenvironment of soil upon manure application using optical sensors

The application of fertilizers and manure on fields is the largest source of ammonia (NH₃) in the atmosphere.·NH₃ emission from agriculture has negative environmental consequences and is largely controlled by the chemical microenvironment and the respective biological activity of the soil. While gas phase and bulk measurements can describe the emission on a large scale, those measurements fail to unravel the local processes and spatial heterogeneity at the soil air interface. We report a two dimensional (2D) imaging approach capable of visualizing three of the most important chemical parameters associated with NH₃ emission from soil. Besides the released NH₃ itself also O₂ and pH microenvironments are imaged using reversible optodes in real-time with a spatial resolution of <100 µm. This combined optode approach utilizes a specifically developed NH₃ optode with a limit of detection of 2.11 ppm and a large working range (0-1800 ppm) ideally suited for studying NH₃ volatilization from soil. This NH₃ optode will contribute to a better understanding of the driving factors for NH₃ emission on a microscale and has the potential to become a valuable tool in studying NH₃ dynamics.

Scanning electrochemical microscopy and its potential for studying biofilms and antimicrobial coatings

Biofilms are known to be well-organized microbial communities embedded in an extracellular polymeric matrix, which supplies bacterial protection against external stressors. Biofilms are widespread and diverse, and despite the considerable large number of publications and efforts reported regarding composition, structure and cell-to-cell communication within biofilms in the last decades, the mechanisms of biofilm formation, the interaction and communication between bacteria are still not fully understood. This knowledge is required to understand why biofilms form and how we can combat them or how we can take advantage of these sessile communities, e.g. in biofuel cells. Therefore, in situ and real-time monitoring of nutrients, metabolites and quorum sensing molecules is of high importance, which may help to fill that knowledge gap. This review focuses on the potential of scanning electrochemical microscopy (SECM) as a versatile method for in situ studies providing temporal and lateral resolution in order to elucidate cell-to-cell communication, microbial metabolism and antimicrobial impact, e.g. of antimicrobial coatings through the study of electrochemical active molecules. Given the complexity and diversity of biofilms, challenges and limitations will be also discussed.

A Minimally Invasive Microsensor Specially Designed for Simultaneous Dissolved Oxygen and pH Biofilm Profiling

A novel sensing device for simultaneous dissolved oxygen (DO) and pH monitoring specially designed for biofilm profiling is presented in this work. This device enabled the recording of instantaneous DO and pH dynamic profiles within biofilms, improving the tools available for the study and the characterization of biological systems. The microsensor consisted of two parallel arrays of microelectrodes. Microelectrodes used for DO sensing were bare gold electrodes, while microelectrodes used for pH sensing were platinum-based electrodes modified using electrodeposited iridium oxide. The device was fabricated with a polyimide (Kapton^®) film of 127 µm as a substrate for minimizing the damage caused on the biofilm structure during its insertion. The electrodes were covered with a Nafion^® layer to increase sensor stability and repeatability and to avoid electrode surface fouling. DO microelectrodes showed a linear response in the range 0–8 mg L⁻¹, a detection limit of 0.05 mg L⁻¹, and a sensitivity of 2.06 nA L mg⁻¹. pH electrodes showed a linear super-Nernstian response (74.2 ± 0.7 mV/pH unit) in a wide pH range (pH 4−9). The multi-analyte sensor array was validated in a flat plate bioreactor where simultaneous and instantaneous pH and DO profiles within a sulfide oxidizing biofilm were recorded. The electrodes spatial resolution, the monitoring sensitivity, and the minimally invasive features exhibited by the proposed microsensor improved biofilm monitoring performance, enabling the quantification of mass transfer resistances and the assessment of biological activity.

In Vitro Community Synergy between Bacterial Soil Isolates Can Be Facilitated by pH Stabilization of the Environment

The composition and development of naturally occurring microbial communities are defined by a complex interplay between the community and the surrounding environment and by interactions between community members. Intriguingly, these interactions can in some cases cause synergies, where the community is able to outperform its single-species constituents. However, the underlying mechanisms driving community interactions are often unknown and difficult to identify due to high community complexity. Here, we show how opposite pH drift induced by specific community members leads to pH stabilization of the microenvironment, acting as a positive interspecies interaction, driving in vitro community synergy in a model consortium of four coisolated soil bacteria, Microbacterium oxydans, Xanthomonas retroflexus, Stenotrophomonas rhizophila, and Paenibacillus amylolyticus We use microsensor pH measurements to show how individual species change the local pH microenvironment and how cocultivation leads to a stabilized pH regime over time. Specifically, in vitro acid production from P. amylolyticus and alkali production primarily from X. retroflexus led to an overall pH stabilization of the local environment over time, which in turn resulted in enhanced community growth. This specific type of interspecies interaction was found to be highly dependent on medium type and concentration; however, similar pH drift from the individual species could be observed across medium variants.IMPORTANCE Understanding interspecies interactions in bacterial communities is important for unraveling species dynamics in naturally occurring communities. These dynamics are fundamental for identifying evolutionary drivers and for the development of efficient biotechnological industry applications. Recently, pH interplay among community members has been identified as a factor affecting community development, and pH stabilization has been demonstrated to result in enhanced community growth. The use of model communities in which the effect of changing pH level can be attributed to specific species contributes to the investigation of community developmental drivers. This contributes to assessment of the extent of emergent behavior and members' contributions to community development. Here, we show that pH stabilization of the microenvironment in vitro in a synthetic coisolated model community results in synergistic growth. This observation adds to the growing diversity of community interactions leading to enhanced community growth and hints toward pH as a strong driver for community development in diverse environments.

Tools for studying growth patterns and chemical dynamics of aggregated Pseudomonas aeruginosa exposed to different electron acceptors in an alginate bead model

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.

Micro-scale H2-CO2 Dynamics in a Hydrogenotrophic Methanogenic Membrane Reactor

Biogas production is a key factor in a sustainable energy supply. It is possible to get biogas with very high methane content if the biogas reactors are supplied with exogenous hydrogen, and one of the technologies for supplying hydrogen is through gas permeable membranes. In this study the activity and stratification of hydrogen consumption above such a membrane was investigated by use of microsensors for hydrogen and pH. A hydrogenotrophic methanogenic community that was able to consume the hydrogen flux within 0.5 mm of the membrane with specific rates of up to 30 m³ H₂ m^-3 day^-1 developed within 3 days in fresh manure and was already established at time zero when analyzing slurry from a biogas plant. The hydrogen consumption was dependent on a simultaneous carbon dioxide supply and was inhibited when carbon dioxide depletion elevated the pH to 9.2. The activity was only partially restored when the carbon dioxide supply was resumed. Bioreactors supplied with hydrogen gas should thus be carefully monitored and either have the hydrogen supply disrupted or be supplemented with carbon dioxide when the pH rises to values about 9.

Oxidation of Molecular Hydrogen by a Chemolithoautotrophic Beggiatoa Strain

A chemolithoautotrophic strain of the family Beggiatoaceae, Beggiatoa sp. strain 35Flor, was found to oxidize molecular hydrogen when grown in a medium with diffusional gradients of oxygen, sulfide, and hydrogen. Microsensor profiles and rate measurements suggested that the strain oxidized hydrogen aerobically when oxygen was available, while hydrogen consumption under anoxic conditions was presumably driven by sulfur respiration.Beggiatoa sp. 35Flor reached significantly higher biomass in hydrogen-supplemented oxygen-sulfide gradient media, but hydrogen did not support growth of the strain in the absence of reduced sulfur compounds. Nevertheless, hydrogen oxidation can provide Beggiatoa sp. 35Flor with energy for maintenance and assimilatory purposes and may support the disposal of internally stored sulfur to prevent physical damage resulting from excessive sulfur accumulation. Our knowledge about the exposure of natural populations of Beggiatoa ceae to hydrogen is very limited, but significant amounts of hydrogen could be provided by nitrogen fixation, fermentation, and geochemical processes in several of their typical habitats such as photosynthetic microbial mats and submarine sites of hydrothermal fluid flow.

IMPORTANCE

Reduced sulfur compounds are certainly the main electron donors for chemolithoautotrophic Beggiatoa ceae, but the traditional focus on this topic has left other possible inorganic electron donors largely unexplored. In this paper, we provide evidence that hydrogen oxidation has the potential to strengthen the ecophysiological plasticity of Beggiatoa ceaein several ways. Moreover, we show that hydrogen oxidation by members of this family can significantly influence biogeochemical gradients and therefore should be considered in environmental studies.

Ratiometric Imaging of Extracellular pH in Dental Biofilms

The pH in bacterial biofilms on teeth is of central importance for dental caries, a disease with a high worldwide prevalence. Nutrients and metabolites are not distributed evenly in dental biofilms. A complex interplay of sorption to and reaction with organic matter in the biofilm reduces the diffusion paths of solutes and creates steep gradients of reactive molecules, including organic acids, across the biofilm. Quantitative fluorescent microscopic methods, such as fluorescence life time imaging or pH ratiometry, can be employed to visualize pH in different microenvironments of dental biofilms. pH ratiometry exploits a pH-dependent shift in the fluorescent emission of pH-sensitive dyes. Calculation of the emission ratio at two different wavelengths allows determining local pH in microscopic images, irrespective of the concentration of the dye. Contrary to microelectrodes the technique allows monitoring both vertical and horizontal pH gradients in real-time without mechanically disturbing the biofilm. However, care must be taken to differentiate accurately between extra- and intracellular compartments of the biofilm. Here, the ratiometric dye, seminaphthorhodafluor-4F 5-(and-6) carboxylic acid (C-SNARF-4) is employed to monitor extracellular pH in in vivo grown dental biofilms of unknown species composition. Upon exposure to glucose the dye is up-concentrated inside all bacterial cells in the biofilms; it is thus used both as a universal bacterial stain and as a marker of extracellular pH. After confocal microscopic image acquisition, the bacterial biomass is removed from all pictures using digital image analysis software, which permits to exclusively calculate extracellular pH. pH ratiometry with the ratiometric dye is well-suited to study extracellular pH in thin biofilms of up to 75 µm thickness, but is limited to the pH range between 4.5 and 7.0.

Ratiometric imaging of extracellular pH in bacterial biofilms with C-SNARF-4

pH in the extracellular matrix of bacterial biofilms is of central importance for microbial metabolism. Biofilms possess a complex three-dimensional architecture characterized by chemically different microenvironments in close proximity. For decades, pH measurements in biofilms have been limited to monitoring bulk pH with electrodes. Although pH microelectrodes with a better spatial resolution have been developed, they do not permit the monitoring of horizontal pH gradients in biofilms in real time. Quantitative fluorescence microscopy can overcome these problems, but none of the hitherto employed methods differentiated accurately between extracellular and intracellular microbial pH and visualized extracellular pH in all areas of the biofilms. Here, we developed a method to reliably monitor extracellular biofilm pH microscopically with the ratiometric pH-sensitive dye C-SNARF-4, choosing dental biofilms as an example. Fluorescent emissions of C-SNARF-4 can be used to calculate extracellular pH irrespective of the dye concentration. We showed that at pH values of <6, C-SNARF-4 stained 15 bacterial species frequently isolated from dental biofilm and visualized the entire bacterial biomass in in vivo-grown dental biofilms with unknown species composition. We then employed digital image analysis to remove the bacterial biomass from the microscopic images and adequately calculate extracellular pH values. As a proof of concept, we monitored the extracellular pH drop in in vivo-grown dental biofilms fermenting glucose. The combination of pH ratiometry with C-SNARF-4 and digital image analysis allows the accurate monitoring of extracellular pH in bacterial biofilms in three dimensions in real time and represents a significant improvement to previously employed methods of biofilm pH measurement.

Development of a rechargeable optical hydrogen peroxide sensor – sensor design and biological application

Measure and recharge!A reversible sensor concept enables repetitive and quantitative measurement of H₂O₂with high spatial and temporal resolution in environmental and biomedical samples.

Marine sediments microbes capable of electrode oxidation as a surrogate for lithotrophic insoluble substrate metabolism

Little is known about the importance and/or mechanisms of biological mineral oxidation in sediments, partially due to the difficulties associated with culturing mineral-oxidizing microbes. We demonstrate that electrochemical enrichment is a feasible approach for isolation of microbes capable of gaining electrons from insoluble minerals. To this end we constructed sediment microcosms and incubated electrodes at various controlled redox potentials. Negative current production was observed in incubations and increased as redox potential decreased (tested −50 to −400 mV vs. Ag/AgCl). Electrode-associated biomass responded to the addition of nitrate and ferric iron as terminal electron acceptors in secondary sediment-free enrichments. Elemental sulfur, elemental iron and amorphous iron sulfide enrichments derived from electrode biomass demonstrated products indicative of sulfur or iron oxidation. The microbes isolated from these enrichments belong to the genera Halomonas, Idiomarina, Marinobacter, and Pseudomonas of the Gammaproteobacteria, and Thalassospira and Thioclava from the Alphaproteobacteria. Chronoamperometry data demonstrates sustained electrode oxidation from these isolates in the absence of alternate electron sources. Cyclic voltammetry demonstrated the variability in dominant electron transfer modes or interactions with electrodes (i.e., biofilm, planktonic or mediator facilitated) and the wide range of midpoint potentials observed for each microbe (from 8 to −295 mV vs. Ag/AgCl). The diversity of extracellular electron transfer mechanisms observed in one sediment and one redox condition, illustrates the potential importance and abundance of these interactions. This approach has promise for increasing our understanding the extent and diversity of microbe mineral interactions, as well as increasing the repository of microbes available for electrochemical applications.

Nanoscale characterization of effect of L-arginine on Streptococcus mutans biofilm adhesion by atomic force microscopy

A major aetiological factor of dental caries is the pathology of the dental plaque biofilms. The amino acid L-arginine (Arg) is found naturally in saliva as a free molecule or as a part of salivary peptides and proteins. Plaque bacteria metabolize Arg to produce alkali and neutralize glycolytic acids, promoting a less cariogenous oral microbiome. Here, we explored an alternative and complementary mechanism of action of Arg using atomic force microscopy. The nanomechanical properties of Streptococcus mutans biofilm extracellular matrix were characterized under physiological buffer conditions. We report the effect of Arg on the adhesive behaviour and structural properties of extracellular polysaccharides in S. mutans biofilms. High-resolution imaging of biofilm surfaces can reveal additional structural information on bacterial cells embedded within the surrounding extracellular matrix. A dense extracellular matrix was observed in biofilms without Arg compared to those grown in the presence of Arg. S. mutans biofilms grown in the presence of Arg could influence the production and/or composition of extracellular membrane glucans and thereby affect their adhesion properties. Our results suggest that the presence of Arg in the oral cavity could influence the adhesion properties of S. mutans to the tooth surface.

Oxygen limitation within a bacterial aggregate

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.

Microsensors and microscale gradients in biofilms

Understanding the limiting factors and mechanisms of biofilm processes requires the direct measurement of microscale gradients using the appropriate tools. Microscale measurements can provide mechanistic information that cannot be obtained from bulk-scale measurements. Among the most used and trusted tools in microscale biofilm research are microsensors. The goal of this chapter is to introduce microsensor technology along with several examples to illustrate microscale processes in biofilms that are usually absent in bulk. We define a microsensor for biofilm research as a needle-type sensor with tip diameter of a few microns and a length up to several hundred microns. Microsensors can be used noninvasively to monitor in situ biofilm processes. Both optical and electrochemical microsensors can be used for biofilm applications. Because of newly discovered biofilm processes, the design and use of microsensors require customization and carefully designed experiments. In this chapter we present several examples describing the use of microsensors (1) in environmental biofilms, (2) in medical biofilms, and (3) in biofilms for energy and bioproducts. Microsensors can be the most useful if the measured profiles are integrated into the study of overall biofilm processes.

Biofilms as living catalysts in continuous chemical syntheses

Biofilms are resilient to a wide variety of environmental stresses. This inherited robustness has been exploited mainly for bioremediation. With a better understanding of their physiology, the application of these living catalysts has been extended to the production of bulk and fine chemicals as well as towards biofuels, biohydrogen, and electricity production in microbial fuel cells. Numerous challenges call for novel solutions and concepts of analytics, biofilm reactor design, product recovery, and scale-up strategies. In this review, we highlight recent advancements in spatiotemporal biofilm characterization and new biofilm reactor developments for the production of value-added fine chemicals as well as current challenges and future scenarios.

A simple optode based method for imaging O2 distribution and dynamics in tap water biofilms

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.

The influence of biofilms on the migration of uranium in acid mine drainage (AMD) waters

The uranium mine in Königstein (Germany) is currently in the process of being flooded. Huge mass of Ferrovum myxofaciens dominated biofilms are growing in the acid mine drainage (AMD) water as macroscopic streamers and as stalactite-like snottites hanging from the ceiling of the galleries. Microsensor measurements were performed in the AMD water as well as in the biofilms from the drainage channel on-site and in the laboratory. The analytical data of the AMD water was used for the thermodynamic calculation of the predominance fields of the aquatic uranium sulfate (UO(2)SO(4)) and UO(2)(++) speciation as well as of the solid uranium species Uranophane [Ca(UO(2))(2)(SiO(3)OH)(2)∙5H(2)O] and Coffinite [U(SiO(4))(1-x)(OH)(4x)], which are defined in the stability field of pH>4.8 and Eh<960 mV and pH>0 and Eh<300 mV, respectively. The plotting of the measured redox potential and pH of the AMD water and the biofilm into the calculated pH-Eh diagram showed that an aqueous uranium(VI) sulfate complex exists under the ambient conditions. According to thermodynamic calculations a retention of uranium from the AMD water by forming solid uranium(VI) or uranium(IV) species will be inhibited until the pH will increase to >4.8. Even analysis by Energy-filtered Transmission Electron Microscopy (EF-TEM) and electron energy loss spectroscopy (EELS) within the biofilms did not provide any microscopic or spectroscopic evidence for the presence of uranium immobilization. In laboratory experiments the first phase of the flooding process was simulated by increasing the pH of the AMD water. The results of the experiments indicated that the F. myxofaciens dominated biofilms may have a substantial impact on the migration of uranium. The AMD water remained acid although it was permanently neutralized with the consequence that the retention of uranium from the aqueous solution by the formation of solid uranium species will be inhibited.

Moonmilk deposits originate from specific bacterial communities in Altamira Cave (Spain)

The influence of bacterial communities on the formation of carbonate deposits such as moonmilk was investigated in Altamira Cave (Spain). The study focuses on the relationship between the bacterial communities at moonmilk deposits and those forming white colonizations, which develop sporadically throughout the cave. Using molecular fingerprinting of the metabolically active bacterial communities detected through RNA analyses, the development of white colonizations and moonmilk deposits showed similar bacterial profiles. White colonizations were able to raise the pH as a result of their metabolism (reaching in situ pH values above 8.5), which was proportional to the nutrient supply. Bacterial activity was analyzed by nanorespirometry showing higher metabolic activity from bacterial colonizations than uncolonized areas. Once carbonate deposits were formed, bacterial activity decreased drastically (down to 5.7% of the white colonization activity). This study reports on a specific type of bacterial community leading to moonmilk deposit formation in a cave environment as a result of bacterial metabolism. The consequence of this process is a macroscopic phenomenon of visible carbonate depositions and accumulation in cave environments.

Combined gel probe and isotope labeling technique for measuring dissimilatory nitrate reduction to ammonium in sediments at millimeter-level resolution

Dissimilatory NO(3)(-) reduction in sediments is often measured in bulk incubations that destroy in situ gradients of controlling factors such as sulfide and oxygen. Additionally, the use of unnaturally high NO(3)(-) concentrations yields potential rather than actual activities of dissimilatory NO(3)(-) reduction. We developed a technique to determine the vertical distribution of the net rates of dissimilatory nitrate reduction to ammonium (DNRA) with minimal physical disturbance in intact sediment cores at millimeter-level resolution. This allows DNRA activity to be directly linked to the microenvironmental conditions in the layer of NO(3)(-) consumption. The water column of the sediment core is amended with (15)NO(3)(-) at the in situ (14)NO(3)(-) concentration. A gel probe is deployed in the sediment and is retrieved after complete diffusive equilibration between the gel and the sediment pore water. The gel is then sliced and the NH(4)(+) dissolved in the gel slices is chemically converted by hypobromite to N(2) in reaction vials. The isotopic composition of N(2) is determined by mass spectrometry. We used the combined gel probe and isotopic labeling technique with freshwater and marine sediment cores and with sterile quartz sand with artificial gradients of (15)NH(4)(+). The results were compared to the NH(4)(+) microsensor profiles measured in freshwater sediment and quartz sand and to the N(2)O microsensor profiles measured in acetylene-amended sediments to trace denitrification.

Differential effects of distinct bacterial biofilms in a cave environment

Current microbial surveys using molecular methods provide us with critical information on the major components of natural bacterial communities. However, limited investigation has been performed on the influence of bacterial metabolism on the environment. In this study, we analyzed the pH generated by distinct bacterial communities in a cave environment. Different bacterial biofilms developing on the walls of the cave were visually distinguished by their colorations (e.g., white, yellow, and gray) and mineral depositions, and previous studies have reported on their bacterial diversity and distribution. Using pH microelectrodes, we carried out in situ measurements and were able to detect differences among these bacterial biofilms. White biofilms and carbonate depositions resulted in alkaline pH values. Gray biofilms also increased the pH although these values remained lower than in white biofilms. A combination of gray-white biofilms resulted in alkaline pH values with highest values at the white edge of the colonies. Yellow biofilms generated a slightly acid pH. These results suggest that different bacterial communities can lead to distinct effects on their environment, for instance, precipitation or dissolution of carbonates in caves. These results add information about metabolic response to current knowledge from bacterial diversity surveys, providing information on the interaction between complex bacterial communities and the geological substrate.

Sulfate-reducing bacteria are common members of bacterial communities in Altamira Cave (Spain)

The conservation of paleolithic paintings such as those in Altamira Cave (Spain) is a primary objective. Recent molecular studies have shown the existence of unknown microbial communities in this cave including anaerobic microorganisms on cave walls. Herein, we analyzed an anaerobic microbial group, the sulfate-reducing bacteria (SRB), from Altamira Cave with potential negative effects on painting conservation. In the present work, the communities of bacteria and SRB were studied through PCR-DGGE analysis. Data suggest that SRB communities represent a significant, highly diverse bacterial group in Altamira Cave. These findings represent a first report on this physiological group on caves with paleolithic paintings and their potential biodegradation consequences. Expanding our knowledge on microbial communities in Altamira Cave is a priority to design appropriate conservation strategies.

Correlated biofilm imaging, transport and metabolism measurements via combined nuclear magnetic resonance and confocal microscopy

Bacterial biofilms are complex, three-dimensional communities found nearly everywhere in nature and are also associated with many human diseases. Detailed metabolic information is critical to understand and exploit beneficial biofilms as well as combat antibiotic-resistant, disease-associated forms. However, most current techniques used to measure temporal and spatial metabolite profiles in these delicate structures are invasive or destructive. Here, we describe imaging, transport and metabolite measurement methods and their correlation for live, non-invasive monitoring of biofilm processes. This novel combination of measurements is enabled by the use of an integrated nuclear magnetic resonance (NMR) and confocal laser scanning microscope (CLSM). NMR methods provide macroscopic structure, metabolic pathway and rate data, spatially resolved metabolite concentrations and water diffusion profiles within the biofilm. In particular, current depth-resolved spectroscopy methods are applied to detect metabolites in 140-190 nl volumes within biofilms of the dissimilatory metal-reducing bacterium Shewanella oneidensis strain MR-1 and the oral bacterium implicated in caries disease, Streptococcus mutans strain UA159. The perfused sample chamber also contains a transparent optical window allowing for the collection of complementary fluorescence information using a unique, in-magnet CLSM. In this example, the entire three-dimensional biofilm structure was imaged using magnetic resonance imaging. This was then correlated to a fluorescent CLSM image by employing a green fluorescent protein reporter construct of S. oneidensis. Non-invasive techniques such as described here, which enable measurements of dynamic metabolic processes, especially in a depth-resolved fashion, are expected to advance our understanding of processes occurring within biofilm communities.

Combined imaging of bacteria and oxygen in biofilms

Transparent sensors for microscopic O(2) imaging were developed by spin coating an ultrathin (<1- to 2-microm) layer of a luminescent O(2) indicator onto coverslips. The sensors showed (i) an ideal Stern-Volmer quenching behavior of the luminescence lifetime towards O(2) levels, (ii) homogeneous measuring characteristics over the sensor surface, and (iii) a linear decline of luminescence lifetime with increasing temperature. When a batch of such coverslip sensors has been characterized, their use is thus essentially calibration free at a known temperature. The sensors are easy to use in flow chambers and other growth devices used in microbiology. We present the first application for combined imaging of O(2) and bacteria in a biofilm flow chamber mounted on a microscope equipped with a spinning-disk confocal unit and a luminescence lifetime camera system.

Nitrogen transformations in stratified aquatic microbial ecosystems

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.