Of microparticles and bacteria identification--(resonance) Raman micro-spectroscopy as a tool for biofilm analysis

Automatic classification of microplastics and natural organic matter mixtures using a deep learning model

Several preprocessing procedures are required for the classification of microplastics (MPs) in aquatic systems using spectroscopic analysis. Procedures such as oxidation, which are employed to remove natural organic matter (NOM) from MPs, can be time- and cost-intensive. Furthermore, the identification process is prone to errors due to the subjective judgment of the operators. Therefore, in this study, deep learning (DL) was applied to improve the classification accuracies for mixtures of microplastic and natural organic matter (MP-NOM). A convolutional neural network (CNN)-based DL model with a spatial attention mechanism was adopted to classify substances from their Raman spectra. Subsequently, the classification results were compared with those obtained using conventional Raman spectral library software to evaluate the applicability of the model. Additionally, the crucial spectral band for training the DL model was investigated by applying gradient-weighted class activation mapping (Grad-CAM) as a post-processing technique. The model achieved an accuracy of 99.54%, which is much higher than the 31.44% achieved by the Raman spectral library. The Grad-CAM approach confirmed that the DL model can effectively identify MPs based on their visually prominent peaks in the Raman spectra. Furthermore, by tracking distinctive spectra without relying solely on visually prominent peaks, we can accurately classify MPs with less prominent peaks, which are characterized by a high standard deviation of intensity. These findings demonstrate the potential for automated and objective classification of MPs without the need for NOM preprocessing, indicating a promising direction for future research in microplastic classification.

Continuous Sizing and Identification of Microplastics in Water

The pollution of the environment with microplastics in general, and in particular, the contamination of our drinking water and other food items, has increasingly become the focus of public attention in recent years. In order to better understand the entry pathways into the human food chain and thus prevent them if possible, a precise characterization of the particles concerning their size and material is indispensable. Particularly small plastic particles pose a special challenge since their material can only be determined by means of large experimental effort. In this work, we present a proof of principle experiment that allows the precise determination of the plastic type and the particle size in a single step. The experiment combines elastic light scattering (Mie scattering) with inelastic light scattering (Raman scattering), the latter being used to determine the plastic type. We conducted Monte Carlo simluations for the elastically scattered light for different kinds of plastics in a microfluidic cuvette which we could reproduce in the experiment. We were able to measure the Raman signals for different microplastics in the same measurement as the elastically scattered light and thereby determine their material. This information was used to select the appropriate Monte Carlo simulation data and to assign the correct particle size to different materials with only one calibration measurement.

A review on characterizing the metabolite property of anammox sludge by spectroscopy

As one of the most promising autotrophic biological nitrogen removal technology, anaerobic ammonia oxidation (anammox) has gained intense attention for the past decades and several full-scale facilities have been implemented worldwide. However, anammox bacteria are easily affected by disturbed external environmental factors, which commonly leads to the fluctuations in reactor performance. The response of anammox sludge to external stress results in changes in components and structural characteristics of intracellular and extracellular polymer substances. Real-time and convenient spectral analysis of anammox sludge metabolites can give early warning of performance deterioration under external stresses, which is of great significance to the stable operation of bioreactor. This review summarized the research progress on characterizing the intracellular and extracellular metabolites of anammox sludge through spectroscopic techniques. The correlation between anammox sludge activity and its key metabolites was analyzed. Also, the limitations and future prospects of applying spectral analytical techniques for anammox bioreactor monitoring were discussed and outlooked. This review may provide valuable information for both scientific study and engineering application of anammox based nitrogen removal technology.

Calcium carbonate deposits and microbial assemblages on microplastics in oligotrophic freshwaters

Microplastics are solid polymer particles with a wide variety of surface properties, found in most waterbodies, and known as carriers of distinct microbial communities affecting the fate of the particles in the environment. Little is known about the formation of mineral deposits on microplastics and how these deposits connect to microbial assemblages and affect the physicochemical properties of the particles. In addition, most of the available research on this topic is based on large microplastics with sizes between 100 μm and up to 5 mm, rather than the small microplastics often found in drinking water sources. To narrow this gap in our understanding of environmental effects on small microplastics, two types of small microplastics made of two distinct polymers, poly(methyl methacrylate) (PMMA) and poly(tetrafluoroethylene) (PTFE) with sizes ranging from 15 to 150 μm, were incubated for six months in unprocessed and processed drinking water with increasing ionic concentration to allow for the formation of mineral deposits and microbial assemblages. Spatially resolved analysis with fluorescent in situ hybridization and confocal Raman microscopic imaging revealed deposits of calcium carbonates and scattered microbial assemblages on all microplastics, with structure, extend, and microbial association with the carbonates depending on the respective microplastic. Notably, PTFE floatation was overcome after three months in unprocessed drinking water but remained unchanged in processed drinking water, whereas PMMA appeared unaffected, indicating that the fate of microplastics in the environment may depend on polymer type and the encountered aquatic conditions forming mineral and microbial attachments to the particle surface.

Advances in Optical Detection of Human-Associated Pathogenic Bacteria

Bacterial infection is a global burden that results in numerous hospital visits and deaths annually. The rise of multi-drug resistant bacteria has dramatically increased this burden. Therefore, there is a clinical need to detect and identify bacteria rapidly and accurately in their native state or a culture-free environment. Current diagnostic techniques lack speed and effectiveness in detecting bacteria that are culture-negative, as well as options for in vivo detection. The optical detection of bacteria offers the potential to overcome these obstacles by providing various platforms that can detect bacteria rapidly, with minimum sample preparation, and, in some cases, culture-free directly from patient fluids or even in vivo. These modalities include infrared, Raman, and fluorescence spectroscopy, along with optical coherence tomography, interference, polarization, and laser speckle. However, these techniques are not without their own set of limitations. This review summarizes the strengths and weaknesses of utilizing each of these optical tools for rapid bacteria detection and identification.

Small Sample Stress: Probing Oxygen-Deprived Ammonia-Oxidizing Bacteria with Raman Spectroscopy In Vivo

The stress response of ammonia-oxidizing bacteria (AOB) to oxygen deprivation limits AOB growth and leads to different nitrification pathways that cause the release of greenhouse gases. Measuring the stress response of AOB has proven to be a challenge due to the low growth rates of stressed AOB, making the sample volumes required to monitor the internal stress response of AOB prohibitive to repeated analysis. In a proof-of-concept study, confocal Raman microscopy with excitation resonant to the heme c moiety of cytochrome c was used to compare the cytochrome c content and activity of stressed and unstressed Nitrosomonas europaea (Nm 50), Nitrosomonas eutropha (Nm 57), Nitrosospira briensis (Nsp 10), and Nitrosospira sp. (Nsp 02) in vivo. Each analysis required no more than 1000 individual cells per sampling; thus, the monitoring of cultures with low cell concentrations was possible. The identified spectral marker delivered reproducible results within the signal-to-noise ratio of the underlying Raman spectra. Cytochrome c content was found to be elevated in oxygen-deprived and previously oxygen-deprived samples. In addition, cells with predominantly ferrous cytochrome c content were found in deprived Nitrosomonas eutropha and Nitrosospira samples, which may be indicative of ongoing electron storage at the time of measurement.

pH-Dependent Conformational Changes of KcsA Tetramer and Monomer Probed by Raman Spectroscopy

KcsA is a tetrameric potassium channel formed out of four identical monomeric subunits used as a standard model for selective potassium transport and pH-dependent gating. Large conformational changes are reported for tetramer and monomer upon gating, and the response of the monomer being controversial with the two major studies partially contradicting each other. KcsA was analyzed as functional tetramers embedded in liposomes and as monomer subunits with confocal Raman microscopy under physiological conditions for the active and the closed channel state, using 532 nm excitation to avoid introducing conformational changes during the measurement. Channel function was confirmed using liposome flux assay. While the classic fingerprint region below 1800 rel. cm⁻¹ in the Raman spectrum of the tetramer was unaffected, the CH-stretching region between 2800 and 3200 rel. cm⁻¹ was found to be strongly affected by the conformation. No pH-dependency was observed in the Raman spectra of the monomer subunits, which closely resembled the Raman spectrum of the tetramer in its active conformation, indicating that the open conformation of the monomer and not the closed conformation as postulated may equal the relaxed state of the molecule.

Raman Sensing and Its Multimodal Combination with Optoacoustics and OCT for Applications in the Life Sciences

Currently, many optical modalities are being investigated, applied, and further developed for non-invasive analysis and sensing in the life sciences. To befit the complexity of the study objects and questions in this field, the combination of two or more modalities is attempted. We review our work on multimodal sensing concepts for applications ranging from non-invasive quantification of biomolecules in the living organism to supporting medical diagnosis showing the combined capabilities of Raman spectroscopy, optical coherence tomography, and optoacoustics.

Microplastics Detection in Streaming Tap Water with Raman Spectroscopy

Microplastic particles have been found in drinking water sources worldwide and, thus, also in our food and beverages. Especially small microplastics, with sizes of 1 mm and less, cannot be identified reliably without spectroscopic means such as Fourier transform infrared spectroscopy (FTIR) or Raman spectroscopy, usually applied to the particles extracted from the samples. However, for drinking and tap water, with its comparatively low biological loads, direct observation may be possible and allows a point-of-entry monitoring for beverages and food to ensure uncontaminated drinking water is being used. In a proof of concept, we apply Raman spectroscopy to observe individual microplastic particles in tap water with added particulate and fluorescent contaminants streaming with 1 L/h through a custom-made flow cell. We evaluated several tubing materials for compatibility with microplastic suspensions containing three different polymers widely found in microplastic surveys worldwide. The experiment promises the monitoring of streaming tap water and even clear surface waters for microplastics smaller than 0.1 mm.

Raman and Surface-Enhanced Raman Scattering for Biofilm Characterization

Biofilms are a communal way of living for microorganisms in which microorganism cells are surrounded by extracellular polymeric substances (EPS). Most microorganisms can live in biofilm form. Since microorganisms are everywhere, understanding biofilm structure and composition is crucial for making the world a better place to live, not only for humans but also for other living creatures. Raman spectroscopy is a nondestructive technique and provides fingerprint information about an analyte of interest. Surface-enhanced Raman spectroscopy is a form of this technique and provides enhanced scattering of the analyte that is in close vicinity of a nanostructured noble metal surface such as silver or gold. In this review, the applications of both techniques and their combination with other biofilm analysis techniques for characterization of composition and structure of biofilms are discussed.

Heat and Bleach: A Cost-Efficient Method for Extracting Microplastics from Return Activated Sludge

The extraction of plastic microparticles, so-called microplastics, from sludge is a challenging task due to the complex, highly organic material often interspersed with other benign microparticles. The current procedures for microplastic extraction from sludge are time consuming and require expensive reagents for density separation as well as large volumes of oxidizing agents for organic removal, often resulting in tiny sample sizes and thus a disproportional risk of sample bias. In this work, we present an improved extraction method tested on return activated sludge (RAS). The treatment of 100 ml of RAS requires only 6% hydrogen peroxide (H₂O₂) for bleaching at 70 °C, followed by density separation with sodium nitrate/sodium thiosulfate (SNT) solution, and is completed within 24 h. Extracted particles of all sizes were chemically analyzed with confocal Raman microscopy. An extraction efficiency of 78 ± 8% for plastic particle sizes 20 µm and up was confirmed in a recovery experiment. However, glass shards with a diameter of less than 20 µm remained in the sample despite the density of glass exceeding the density of the separating SNT solution by 1.1 g/cm³. This indicates that density separation may be unreliable for particle sizes in the lower micrometer range.

Confocal Raman microscopy and fluorescent in situ hybridization - A complementary approach for biofilm analysis

We combine confocal Raman microscopy (CRM) of wet samples with subsequent Fluorescent in situ hybridization (FISH) without significant limitations to either technique for analyzing the same sample of a microbial community on a cell-to-cell basis. This combination of techniques allows a much deeper, more complete understanding of complex environmental samples than provided by either technique alone. The minimalistic approach is based on laboratory glassware with micro-engravings for reproducible localization of the sample at cell scale combined with a fixation and de- and rehydration protocol for the respective techniques. As proof of concept, we analyzed a floc of nitrifying activated sludge, demonstrating that the sample can be tracked with cell-scale precision over different measurements and instruments. The collected information includes the microbial content, spatial shape, variant chemical compositions of the floc matrix and the mineral microparticles embedded within. In addition, the direct comparison of CRM and FISH revealed a difference in reported cell size due to the different cell components targeted by the respective technique. To the best of our knowledge, this is the first report of a direct cell-to-cell comparison of confocal Raman microscopy and Fluorescent in situ hybridization analysis performed on the same sample. An adaptation of the method to include native samples as a starting point is planned for the near future. The micro-engraving approach itself also opens up the possibility of combining other, functionally incompatible techniques as required for further in-depth investigations of low-volume samples.

In Situ Analysis of a Silver Nanoparticle-Precipitating Shewanella Biofilm by Surface Enhanced Confocal Raman Microscopy

Shewanella oneidensis MR-1 is an electroactive bacterium, capable of reducing extracellular insoluble electron acceptors, making it important for both nutrient cycling in nature and microbial electrochemical technologies, such as microbial fuel cells and microbial electrosynthesis. When allowed to anaerobically colonize an Ag/AgCl solid interface, S. oneidensis has precipitated silver nanoparticles (AgNp), thus providing the means for a surface enhanced confocal Raman microscopy (SECRaM) investigation of its biofilm. The result is the in-situ chemical mapping of the biofilm as it developed over time, where the distribution of cytochromes, reduced and oxidized flavins, polysaccharides and phosphate in the undisturbed biofilm is monitored. Utilizing AgNp bio-produced by the bacteria colonizing the Ag/AgCl interface, we could perform SECRaM while avoiding the use of a patterned or roughened support or the introduction of noble metal salts and reducing agents. This new method will allow a spatially and temporally resolved chemical investigation not only of Shewanella biofilms at an insoluble electron acceptor, but also of other noble metal nanoparticle-precipitating bacteria in laboratory cultures or in complex microbial communities in their natural habitats.

Isolation and identification of bacteria by means of Raman spectroscopy

Bacterial detection is a highly topical research area, because various fields of application will benefit from the progress being made. Consequently, new and innovative strategies which enable the investigation of complex samples, like body fluids or food stuff, and improvements regarding the limit of detection are of general interest. Within this review the prospects of Raman spectroscopy as a reliable tool for identifying bacteria in complex samples are discussed. The main emphasis of this work is on important aspects of applying Raman spectroscopy for the detection of bacteria like sample preparation and the identification process. Several approaches for a Raman compatible isolation of bacterial cells have been developed and applied to different matrices. Here, an overview of the limitations and possibilities of these methods is provided. Furthermore, the utilization of Raman spectroscopy for diagnostic purposes, food safety and environmental issues is discussed under a critical view.

Phototrophic bacteria for nutrient recovery from domestic wastewater

The organics and nutrients in industrial and domestic wastewater are increasingly being regarded as a valuable resource for energy and nutrient recovery. Emerging concepts to redesign wastewater treatment as resource recovery systems include the use of different bacteria and algae to partition carbon and nutrients to the particulate phase through assimilation or bio-accumulation. This study evaluates the use of purple phototrophic bacteria (PPB) (also known as purple non-sulphur bacteria or PNSB) for such a biological concentration process through a series of batch tests. The key objectives are to (a) demonstrate consistent selection and enrichment of PPB using infrared light in a non-sterile medium, and (b) achieve effective partitioning of soluble organics, ammonium and phosphate into the PPB culture. PPB were successfully enriched from pre-settled domestic wastewater within 2-3 days and identified as members of the order Rhodobacterales. Under anaerobic conditions with infrared irradiation the enrichment culture was able to simultaneously remove COD (63 ± 5%), NH4-N (99.6%-0.12 ± 0.03 mgN L(-1)) and PO4-P (88%-0.8 ± 0.6 mgP L(-1)) from primary settled domestic wastewater in 24 h. In this experiment, acetate was added as an additional carbon source to demonstrate the maximal nitrogen and phosphorous elimination potential. Almost all the COD removed was assimilated into biomass rather than oxidised to CO2, with the total COD actually increasing during the batch experiments due to phototrophic synthesis. NH4-N and PO4-P were also assimilated by the biomass rather than removed through destructive oxidation or accumulation. The process offers the opportunity to concentrate organics and macronutrients from wastewater in one solids stream that can be anaerobically digested to generate energy and recover nutrients from the concentrated digestate. Technical challenges include the design of a continuous reactor system, as well as efficient delivery of electrons, either through light or chemical sources.

Microbial relevant fouling in membrane bioreactors: influencing factors, characterization, and fouling control

Microorganisms in membrane bioreactors (MBRs) play important roles on degradation of organic/inorganic substances in wastewaters, while microbial deposition/growth and microbial product accumulation on membranes potentially induce membrane fouling. Generally, there is a need to characterize membrane foulants and to determine their relations to the evolution of membrane fouling in order to identify a suitable fouling control approach in MBRs. This review summarized the factors in MBRs that influence microbial behaviors (community compositions, physical properties, and microbial products). The state-of-the-art techniques to characterize biofoulants in MBRs were reported. The strategies for controlling microbial relevant fouling were discussed and the future studies on membrane fouling mechanisms in MBRs were proposed.