Exploring the Potential of Stable Isotope (Resonance) Raman Microspectroscopy and Surface-Enhanced Raman Scattering for the Analysis of Microorganisms at Single Cell Level

Reverse stable isotope labelling with Raman spectroscopy for microbial proteomics

Global proteome changes in microbes affect the survival and overall production of commercially relevant metabolites through different bioprocesses. The existing methods to monitor proteome level changes are destructive in nature. Stable isotope probing (SIP) coupled with Raman spectroscopy is a relatively new approach for proteome analysis. However, applying this approach for monitoring changes in a large culture volume is not cost-effective. In this study, for the first time we are presenting a novel method of combining reverse SIP using 13 C-glucose and Deuterium to monitor the proteome changes through Raman spectroscopy. The findings of the study revealed visible changes (blue shifts) in proteome related peaks that can be used for monitoring proteome dynamics, that is, synthesis of nascent amino acids and its turnover with time in a non-destructive, cost-effective, and label-free manner.

Monitoring of microbial proteome dynamics using Raman stable isotope probing

Abnormal protein kinetics could be a cause of several diseases associated with essential life processes. An accurate understanding of protein dynamics and turnover is essential for developing diagnostic or therapeutic tools to monitor these changes. Raman spectroscopy in combination with stable isotope probes (SIP) such as carbon-13, and deuterium has been a breakthrough in the qualitative and quantitative study of various metabolites. In this work, we are reporting the utility of Raman-SIP for monitoring dynamic changes in the proteome at the community level. We have used ¹³ C-labeled glucose as the only carbon source in the medium and verified its incorporation in the microbial biomass in a time-dependent manner. A visible redshift in the Raman spectral vibrations of major biomolecules such as nucleic acids, phenylalanine, tyrosine, amide I, and amide III were observed. Temporal changes in the intensity of these bands demonstrating the feasibility of protein turnover monitoring were also verified. Kanamycin, a protein synthesis inhibitor was used to assess the feasibility of identifying effects on protein turnover in the cells. Successful application of this work can provide an alternate/adjunct tool for monitoring proteome-level changes in an objective and nondestructive manner.

Electrochemically assisted wide area Raman with standard curved surface quantification method

Reproducibility is still a great challenge for surface-enhanced Raman scattering (SERS), because the uncontrollable fabrication of SERS substrates or the uneven distribution of samples on the substrate result in the signal fluctuation with or between the substrates. Herein, a novel SERS quantitative method with good reproducibility was proposed. It is based on the basic principle that the SERS signal intensity is not only related to electromagnetic enhancement and the concentration of sample, but also related to the specific surface area of the substrate. The surface area information of the substrate is obtained through electrochemical technology, and then introduced into the standard curve with the linear relationship of concentration of sample and SERS intensity as a new variable to obtain a 3D standard curved surface, which effectively corrects the signal difference between the substrates, and combines the wide area Raman method to reduce the difference within the substrate, thereby improving the reproducibility of SERS quantitative detection. Using malachite green (MG) as the probe molecule and using cyclic voltammetry to calculate the substrate area fitted plane model (CV-standard curved surface), the root mean square error (RMSE) of the predicted result is 0.26 and the relative error (RE) is 0.25. It shows that the detection error significantly reduces comparing with the traditional standard curve method. Also, the proposed method can be used in other SERS quantitative detection and has potential application prospects.

Multi-element stable isotope Raman microspectroscopy of bacterial carotenoids unravels rare signal shift patterns and single-cell phenotypic heterogeneity

Investigation of bacteria with D-carotenoids reveals unique Raman signatures, inclusive unexpected blue-shift. Simultaneous monitoring of 13C & D of carotenoids provides complementary information on cell growth and metabolic activity, respectively.

Hyperglycemia and cancer in human lung carcinoma by means of Raman spectroscopy and imaging

Raman spectroscopy and Raman imaging were used to identify the biochemical and structural features of human cancer lung cells (CCL-185) and the cancer cells supplemented with glucose and deuterated glucose at normal and hyperglycemia conditions. We found that isotope substitution of glucose by deuterated glucose allows to separate de novo lipid synthesis from exogenous uptake of lipids obtained from the diet. We demonstrated that glucose is largely utilized for de novo lipid synthesis. Our results provide a direct evidence that high level of glucose decreases the metabolism via oxidative phosphorylation in mitochondria in cancer cells and shifts the metabolism to glycolysis via Warburg effect. It suggests that hyperglycemia is a factor that may contribute to a more malignant phenotype of cancer cells by inhibition of oxidative phosphorylation and apoptosis.

Metabolic characteristics and markers in viable but nonculturable state of Pseudomonas aeruginosa induced by chlorine stress

Many Gram-negative pathogens enter the viable but nonculturable (VBNC) state to resist external environmental stress (such as disinfection). However, little is known about the metabolic properties, especially for the metabolic markers, of VBNC bacteria, which impedes the development of efficient disinfection technologies and causes more potential health risks. In this study, we analyzed the metabolic characteristics of chlorine stress-induced VBNC Pseudomonas aeruginosa at the population and single-cell levels. The overall metabolic activity of VBNC bacteria showed a downward trend, but the glyoxylate cycle, fatty acid and glycerophospholipid metabolism pathways were up-regulated. Based on the metabolic profiles of VBNC bacteria, nine metabolic markers (pyruvate, glyoxylate, guanine, glutamate, sn glycero-3-phos-phocholine, fatty acid, D-alanine, glutathione, N-Butanoyl-D-homoserine lactone) were determined. The results of single-cell Raman spectroscopy showed that the metabolic activity of VBNC bacteria was significantly reduced, but showed more significant metabolic heterogeneity. The redshift of the Raman peaks of ¹⁵N and ¹³C labeled VBNC bacteria was significantly weaker than that of the culturable bacteria, suggesting that the VBNC bacteria have a reduced ability to synthesize proteins, nucleotides, phospholipids, and carbohydrates. The result of this study can help to better understand the metabolic mechanisms and energy management strategy of VBNC bacteria, to achieve precise identification and effective control of VBNC bacteria.

Single-cell metagenomics and metagenomics approaches reveal extracellular electron transfer of psychrophilic electroactive biofilms

Revealing the metabolic functions and the extracellular electron transfer (EET) process of psychrophilic electroactive biofilms (PEB) is important for understanding the functional adaptability of electroactive bacteria (EAB) to low temperatures. In this study, single cell sorting (SCS)-based metagenomics sequencing was used to characterize the composition and function of the PEB. Biofilm microbiome analysis showed that Geobacter, with a relative abundance of 62.64%, dominated the PEB enriched in the bioelectrochemical system (BES) at 4 °C. Both the metagenome (MAG) and single-cell metagenome (SCM) revealed that there were no obvious metabolic differences between the original biofilm and the sorted single cells. The presence of genes associated with type IV pilus, c-type cytochromes, and riboflavin indicated that the EET potential was maintained in the PEB at low temperatures. These results suggested that SCM provides an alternative approach to reconstruct the metabolic functions of uncultured and slow-growing EAB.

Probing the Biogenesis of Polysaccharide Granules in Algal Cells at Sub-Organellar Resolution via Raman Microscopy with Stable Isotope Labeling

Phototrophs assimilate CO₂ into organic compounds that accumulate in storage organelles. Elucidation of the carbon dynamics of storage organelles could enhance the production efficiency of valuable compounds and facilitate the screening of strains with high photosynthetic activity. To comprehensively elucidate the carbon dynamics of these organelles, the intraorganellar distribution of the carbon atoms that accumulate at specific time periods should be probed. In this study, the biosynthesis of polysaccharides in storage organelles was spatiotemporally probed via stimulated Raman scattering (SRS) microscopy using a stable isotope (¹³C) as the tracking probe. Paramylon granules (a storage organelle of β-1,3-glucan) accumulated in a unicellular photosynthetic alga, Euglena gracilis, were investigated as a model organelle. The carbon source of the culture medium was switched from NaH¹²CO₃ to NaH¹³CO₃ during the production of the paramylon granules; this resulted in the distribution of the ¹²C and ¹³C constituents in the granules, so that the biosynthetic process could be tracked. Taking advantage of high-resolution SRS imaging and label switching, the localization of the ¹²C and ¹³C constituents inside a single paramylon granule could be visualized in three dimensions, thus revealing the growth process of paramylon granules. We propose that this method can be used for comprehensive elucidation of the dynamic activities of storage organelles.

Using Stable Isotope Probing and Raman Microspectroscopy To Measure Growth Rates of Heterotrophic Bacteria

The suitability of stable isotope probing (SIP) and Raman microspectroscopy to measure growth rates of heterotrophic bacteria at the single-cell level was evaluated. Label assimilation into Escherichia coli biomass during growth on a complex ¹³C-labeled carbon source was monitored in time course experiments. ¹³C incorporation into various biomolecules was measured by spectral "red shifts" of Raman-scattered emissions. The ¹³C- and ¹²C-isotopologues of the amino acid phenylalanine (Phe) proved to be quantitatively accurate reporter molecules of cellular isotopic fractional abundances (f_cell). Values of f_cell determined by Raman microspectroscopy and independently by isotope ratio mass spectrometry (IRMS) over a range of isotopic enrichments were statistically indistinguishable. Progressive labeling of Phe in E. coli cells among a range of ¹³C/¹²C organic substrate admixtures occurred predictably through time. The relative isotopologue abundances of Phe determined by Raman spectral analysis enabled the accurate calculation of bacterial growth rates as confirmed independently by optical density (OD) measurements. The results demonstrate that combining SIP and Raman microspectroscopy can be a powerful tool for studying bacterial growth at the single-cell level on defined or complex organic ¹³C carbon sources, even in mixed microbial assemblages. IMPORTANCE Population growth dynamics and individual cell growth rates are the ultimate expressions of a microorganism's fitness under its environmental conditions, whether natural or engineered. Natural habitats and many industrial settings harbor complex microbial assemblages. Their heterogeneity in growth responses to existing and changing conditions is often difficult to grasp by standard methodologies. In this proof-of-concept study, we tested whether Raman microspectroscopy can reliably quantify the assimilation of isotopically labeled nutrients into E. coli cells and enable the determination of individual growth rates among heterotrophic bacteria. Raman-derived growth rate estimates were statistically indistinguishable from those derived by standard optical density measurements of the same cultures. Raman microspectroscopy can also be combined with methods for phylogenetic identification. We report the development of Raman-based techniques that enable researchers to directly link genetic identity to functional traits and rate measurements of single cells within mixed microbial assemblages, currently a major technical challenge in microbiological research.

Raman Stable Isotope Probing of Bacteria in Visible and Deep UV-Ranges

Raman stable isotope probing (Raman-SIP) is an excellent technique that can be used to access the overall metabolism of microorganisms. Recent studies have mainly used an excitation wavelength in the visible range to characterize isotopically labeled bacteria. In this work, we used UV resonance Raman spectroscopy (UVRR) to evaluate the spectral red-shifts caused by the uptake of isotopes (¹³C, ¹⁵N, ²H(D) and ¹⁸O) in E. coli cells. Moreover, we present a new approach based on the extraction of labeled DNA in combination with UVRR to identify metabolically active cells. The proof-of-principle study on E. coli revealed heterogeneities in the Raman features of both the bacterial cells and the extracted DNA after labeling with ¹³C, ¹⁵N, and D. The wavelength of choice for studying ¹⁸O- and deuterium-labeled cells is 532 nm is, while ¹³C-labeled cells can be investigated with visible and deep UV wavelengths. However, ¹⁵N-labeled cells are best studied at the excitation wavelength of 244 nm since nucleic acids are in resonance at this wavelength. These results highlight the potential of the presented approach to identify active bacterial cells. This work can serve as a basis for the development of new techniques for the rapid and efficient detection of active bacteria cells without the need for a cultivation step.

Raman 18 O-labeling of bacteria in visible and deep UV-ranges

Raman stable isotope labeling with ² H, ¹³ C or ¹⁵ N has been reported as an elegant approach to investigate cellular metabolic activity, which is of great importance to reveal the functions of microorganisms in native environments. A new strategy termed Raman ¹⁸ O-labeling was developed to probe the metabolic activity of bacteria. Raman ¹⁸ O-labeling refers to the combination of Raman microspectroscopy with ¹⁸ O-labeling using H₂¹⁸ O. At an excitation wavelength of 532 nm, the incorporation of ¹⁸ O into the amide I group of proteins and DNA/RNA bases was observed in Escherichia coli cells, while for an excitation wavelength electronically resonant with DNA or aromatic amino acid absorption at 244 nm ¹⁸ O assimilation was detected using chemometric tools rather than visual inspection. Raman ¹⁸ O-labeling at 532 nm combined with 2D correlation analysis confirmed the assimilation of ¹⁸ O in proteins and nucleic acids and revealed the growth strategy of E. coli cells; they underwent protein synthesis followed by nucleic acid synthesis. Independent cultural replicates at different incubation times corroborated the reproducibility of these results. The variations in spectral features of ¹⁸ O-labeled cells revealed changes in physiological information of cells. Hence, Raman ¹⁸ O-labeling could provide a powerful tool to identify metabolically active bacterial cells.

Opening up the Single-Cell Toolbox for Microbial Natural Products Research

The diverse microbes that produce natural products represent an important source of novel therapeutics, drug leads, and scientific tools. However, the vast majority have not been grown in axenic culture and are members of complex communities. While meta-'omic methods such as metagenomics, -transcriptomics, and -proteomics reveal collective molecular features of this "microbial dark matter", the study of individual microbiome members can be challenging. To address these limits, a number of techniques with single-bacterial resolution have been developed in the last decade and a half. While several of these are embraced by microbial ecologists, there has been less use by researchers interested in mining microbes for natural products. In this review, we discuss the available and emerging techniques for targeted single-cell analysis with a particular focus on applications to the discovery and study of natural products.

Mini-metagenome analysis of psychrophilic electroactive biofilms based on single cell sorting

Understanding the metabolic function of psychrophilic electroactive bacteria is important for the investigation of extracellular electron transfer (EET) mechanisms under low temperatures (4-15 °C). In this study, Raman activated cell ejection coupled high throughput sequencing was used to accurately generate a mini-metagenome of psychrophilic bacterial community. Hierarchical cluster analysis of the Raman spectrum could accurately select the target Geobacter cluster. The high relative abundance of the membrane transport functional genes ftsEX in the biofilm community indicated an adaptation to reduced temperature, which aided survival of the electroactive bacteria under low temperature. The basal metabolism such as citrate cycle and glycolytic pathway maintained the electron pool for the EET process. The identification of iron (III) transport system genes in high abundance indicated their presence in an active metabolic reaction for potential electron transfer process. It showed the potential involvement c-type cytochromes (coxA and cox1) activity in EET. These results indicated that psychrophilic Geobacter had effective EET mediated by c-type cytochromes at low temperatures.

Metabolism in action: stable isotope probing using vibrational spectroscopy and SIMS reveals kinetic and metabolic flux of key substrates

Microbial communities play essential functions which drive various ecosystems supporting animal and aquatic life. However, linking bacteria with specific metabolic functions is difficult, since microbial communities consist of numerous and phylogenetically diverse microbes. Stable isotope probing (SIP) combined with single-cell tools has emerged as a novel culture-independent strategy for unravelling microbial metabolic roles and intertwined interactions in complex communities. In this study, we applied Raman and Fourier-transform infrared (FT-IR) spectroscopies, secondary ion mass spectrometry (SIMS) with SIP to probe the rate of ¹³C incorporation in Escherichia coli at 37 and 25 °C. Our results indicate quantitative enrichment and flow of ¹³C into E. coli at various time points. Multivariate and univariate analyses of Raman and FT-IR data demonstrated distinctive ¹³C concentration-dependent trends that were due to vibrational bands shifting to lower frequencies and these shifts were a result of incubation time and metabolic rate. SIMS results were in complete agreement with the spectroscopy findings, and confirmed the detected levels of ¹³C incorporation into microbial biomass at the investigated conditions. Having established that FT-IR and Raman spectroscopy with SIP can measure metabolism kinetics in this simple system, we have applied the kinetics concept to study the metabolism of phenol by Pseudomonas putida and metabolic interactions within a two-species consortia with E. coli that could not degrade phenol. Raman spectroscopy combined with SIP identified quantitative shifts in P. putida due to temporal assimilation of phenol. Although E. coli was unable to grow on phenol, in co-culture with P. putida, general metabolic probing using deuterated water for SIP revealed that E. coli displayed increasing metabolic activity, presumably due to cross feeding from metabolites generated by P. putida. This study clearly demonstrates that Raman and FT-IR combined with SIP provide rapid and sensitive detection of carbon incorporation rates and microbial interactions. These novel findings may guide the identification of primary substrate consumers in complex microbial communities in situ, which is a key step towards the characterisation of novel genes, enzymes and metabolic flux analysis in microbial consortia.

Improvement of Surface-Enhanced Raman Scattering Method for Single Bacterial Cell Analysis

Surface-enhanced Raman scattering (SERS) is a useful tool for label-free analysis of bacteria at the single cell level. However, low reproducibility limits the use of SERS. In this study, for the sake of sensitive and reproducible Raman spectra, we optimized the methods for preparing silver nanoparticles (AgNPs) and depositing AgNPs onto a cell surface. We found that fast dropwise addition of AgNO₃ into the reductant produced smaller and more stable AgNPs, with an average diameter of 45 ± 4 nm. Compared with that observed after simply mixing the bacterial cells with AgNPs, the SERS signal was significantly improved after centrifugation. To optimize the SERS enhancement method, the centrifugal force, method for preparing AgNPs, concentration of AgNPs, ionic strength of the solution used to suspend the cells, and density of the cells were chosen as impact factors and optimized through orthogonal experiments. Finally, the improved method could generate sensitive and reproducible SERS spectra from single Escherichia coli cells, and the SERS signals primarily arose from the cell envelope. We further verified that this optimal method was feasible for the detection of low to 25% incorporation of ¹³C isotopes by the cells and the discrimination of different bacterial species. Our work provides an improved method for generating sensitive and reproducible SERS spectra.

Towards Reliable and Quantitative Surface-Enhanced Raman Scattering (SERS): From Key Parameters to Good Analytical Practice

Experimental results obtained in different laboratories world-wide by researchers using surface-enhanced Raman scattering (SERS) can differ significantly. We, an international team of scientists with long-standing expertise in SERS, address this issue from our perspective by presenting considerations on reliable and quantitative SERS. The central idea of this joint effort is to highlight key parameters and pitfalls that are often encountered in the literature. To that end, we provide here a series of recommendations on: a) the characterization of solid and colloidal SERS substrates by correlative electron and optical microscopy and spectroscopy, b) on the determination of the SERS enhancement factor (EF), including suitable Raman reporter/probe molecules, and finally on c) good analytical practice. We hope that both newcomers and specialists will benefit from these recommendations to increase the inter-laboratory comparability of experimental SERS results and further establish SERS as an analytical tool.

Next-generation physiology approaches to study microbiome function at single cell level

The function of cells in their native habitat often cannot be reliably predicted from genomic data or from physiology studies of isolates. Traditional experimental approaches to study the function of taxonomically and metabolically diverse microbiomes are limited by their destructive nature, low spatial resolution or low throughput. Recently developed technologies can offer new insights into cellular function in natural and human-made systems and how microorganisms interact with and shape the environments that they inhabit. In this Review, we provide an overview of these next-generation physiology approaches and discuss how the non-destructive analysis of cellular phenotypes, in combination with the separation of the target cells for downstream analyses, provide powerful new, complementary ways to study microbiome function. We anticipate that the widespread application of next-generation physiology approaches will transform the field of microbial ecology and dramatically improve our understanding of how microorganisms function in their native environment.

Spatiotemporal monitoring of intracellular metabolic dynamics by resonance Raman microscopy with isotope labeling

We probed production process of a cellular metabolite with a stable isotope-labeled substrate exposed to various conditions.

Surface-enhanced Raman spectroscopy of microorganisms: limitations and applicability on the single-cell level

Detection and characterization of microorganisms is essential for both clinical diagnostics and environmental studies. An emerging technique to analyse microbes at single-cell resolution is surface-enhanced Raman spectroscopy (surface-enhanced Raman scattering: SERS). Optimised SERS procedures enable fast analytical read-outs with specific molecular information, providing insight into the chemical composition of microbiological samples. Knowledge about the origin of microbial SERS signals and parameter(s) affecting their occurrence, intensity and/or reproducibility is crucial for reliable SERS-based analyses. In this work, we explore the feasibility and limitations of the SERS approach for characterizing microbial cells and investigate the applicability of SERS for single-cell sorting as well as for three-dimensional visualization of microbial communities. Analyses of six different microbial species (an archaeon, two Gram-positive bacteria, three Gram-negative bacteria) showed that for several of these organisms distinct features in their SERS spectra were lacking. As additional confounding factor, the physiological conditions of the cells (as influenced by e.g., storage conditions or deuterium-labelling) were systematically addressed, for which we conclude that the respective SERS signal at the single-cell level is strongly influenced by the metabolic activity of the analysed cells. While this finding complicates the interpretation of SERS data, it may on the other hand enable probing of the metabolic state of individual cells within microbial populations of interest.

pKa Determination of a Histidine Residue in a Short Peptide Using Raman Spectroscopy

Determining the pKa of key functional groups is critical to understanding the pH-dependent behavior of biological proteins and peptide-based biomaterials. Traditionally, ¹H NMR spectroscopy has been used to determine the pKa of amino acids; however, for larger molecules and aggregating systems, this method can be practically impossible. Previous studies concluded that the C-D stretches in Raman are a useful alternative for determining the pKa of histidine residues. In this study, we report on the Raman application of the C2-D probe on histidine’s imidazole side chain to determining the pKa of histidine in a short peptide sequence. The pKa of the tripeptide was found via difference Raman spectroscopy to be 6.82, and this value was independently confirmed via ¹H NMR spectroscopy on the same peptide. The C2-D probe was also compared to other Raman reporters of the protonation state of histidine and was determined to be more sensitive and reliable than other protonation-dependent signals. The C2-D Raman probe expands the tool box available to chemists interested in directly interrogating the pKa’s of histidine-containing peptide and protein systems.

Stable Isotope-Labeled Single-Cell Raman Spectroscopy Revealing Function and Activity of Environmental Microbes

Microorganisms play a key role in driving the global element (C, N, H, P, and S) cycling. However, the function and activity of environmental microbes remain largely elusive because the vast majority of them are yet uncultured. Recent achievements in single cell stable isotope-labeled Raman spectroscopy enable direct investigation of function and activity of individual microbes in complex environmental communities. Here, this protocol describes a workflow to investigate environmental microbes in soil and water by combining ¹⁵N, ²D, and ¹³C stable isotope labeling with different single-cell Raman techniques, including normal Raman, resonance Raman (RR), and surface-enhanced Raman spectroscopy (SERS). Their applications in investigating functional bacteria driving the N and C cycles, and metabolically active cells are described.

Synthesis and Postpolymerization Modification of Fluorine-End-Labeled Poly(Pentafluorophenyl Methacrylate) Obtained via RAFT Polymerization

Chain-end-labeled polymers are interesting for a range of applications. In polymer nanomedicine, chain-end-labeled polymers are useful to study and help understand cellular internalization and intracellular trafficking processes. The recent advent of fluorescent label-free techniques, such as nanoscale secondary ion mass spectrometry (NanoSIMS), provides access to high-resolution intracellular mapping that can complement information obtained using fluorescent-labeled materials and confocal microscopy and flow cytometry. Using poly(N-(2-hydroxypropyl)methacrylamide) (PHPMA) as a prototypical polymer nanomedicine, this paper presents a synthetic strategy to polymers that contain trace element labels, such as fluorine, which can be used for NanoSIMS analysis. The strategy presented in this paper is based on reversible addition fragmentation chain transfer (RAFT) polymerization of pentafluorophenyl methacrylate (PFMA) mediated by two novel chain-transfer agents (CTAs), which contain either one (α) or two (α,ω) fluorine labels. In the first part of this study, via a number of polymerization experiments, the polymerization properties of the fluorinated RAFT CTAs were established. 19F NMR spectroscopy revealed that these fluorinated RAFT agents possess unique spectral signatures, which allow to directly monitor RAFT agent conversion and measure end-group fidelity. Comparison with 4-cyanopentanoic acid dithiobenzoate, which is a standard CTA for the RAFT polymerization of PFMA, revealed that the introduction of one or two fluorine labels does not significantly affect the polymerization properties of the CTA. In the last part of this paper, a proof-of-concept study is presented that demonstrates the feasibility of the fluorine-labeled poly(pentafluorophenyl methacrylate) polymers as platforms for the postpolymerization modification to generate PHPMA-based polymer nanomedicines.

Surface-Enhanced Raman Scattering (SERS) in Microbiology: Illumination and Enhancement of the Microbial World

The microbial world forms a huge family of organisms that exhibit the greatest phylogenetic diversity on Earth and thus colonize virtually our entire planet. Due to this diversity and subsequent complex interactions, the vast majority of microorganisms are involved in innumerable natural bioprocesses and contribute an absolutely vital role toward the maintenance of life on Earth, whilst a small minority cause various infectious diseases. The ever-increasing demand for environmental monitoring, sustainable ecosystems, food security, and improved healthcare systems drives the continuous search for inexpensive but reproducible, automated and portable techniques for detection of microbial isolates and understanding their interactions for clinical, environmental, and industrial applications and benefits. Surface-enhanced Raman scattering (SERS) is attracting significant attention for the accurate identification, discrimination and characterization and functional assessment of microbial cells at the single cell level. In this review, we briefly discuss the technological advances in Raman and Fourier transform infrared (FT-IR) instrumentation and their application for the analysis of clinically and industrially relevant microorganisms, biofilms, and biological warfare agents. In addition, we summarize the current trends and future prospects of integrating Raman/SERS-isotopic labeling and cell sorting technologies in parallel, to link genotype-to-phenotype in order to define community function of unculturable microbial cells in mixed microbial communities which possess admirable traits such as detoxification of pollutants and recycling of essential metals.

Functional Single-Cell Approach to Probing Nitrogen-Fixing Bacteria in Soil Communities by Resonance Raman Spectroscopy with 15N2 Labeling

Nitrogen (N) fixation is the conversion of inert nitrogen gas (N₂) to bioavailable N essential for all forms of life. N₂-fixing microorganisms (diazotrophs), which play a key role in global N cycling, remain largely obscure because a large majority are uncultured. Direct probing of active diazotrophs in the environment is still a major challenge. Herein, a novel culture-independent single-cell approach combining resonance Raman (RR) spectroscopy with ¹⁵N₂ stable isotope probing (SIP) was developed to discern N₂-fixing bacteria in a complex soil community. Strong RR signals of cytochrome c (Cyt c, frequently present in diverse N₂-fixing bacteria), along with a marked ¹⁵N₂-induced Cyt c band shift, generated a highly distinguishable biomarker for N₂ fixation. ¹⁵N₂-induced shift was consistent well with ¹⁵N abundance in cell determined by isotope ratio mass spectroscopy. By applying this biomarker and Raman imaging, N₂-fixing bacteria in both artificial and complex soil communities were discerned and imaged at the single-cell level. The linear band shift of Cyt c versus ¹⁵N₂ percentage allowed quantification of N₂ fixation extent of diverse soil bacteria. This single-cell approach will advance the exploration of hitherto uncultured diazotrophs in diverse ecosystems.

Stable isotope compounds - production, detection, and application

Stable isotopes are used in wide fields of application from natural tracers in biology, geology and archeology through studies of metabolic fluxes to their application as tracers in quantitative proteomics and structural biology. We review the use of stable isotopes of biogenic elements (H, C, N, O, S, Mg, Se) with the emphasis on hydrogen and its heavy isotope deuterium. We will discuss the limitations of enriching various compounds in stable isotopes when produced in living organisms. Finally, we overview methods for measuring stable isotopes, focusing on methods for detection in single cells in situ and their exploitation in modern biotechnologies.

Application of stable-isotope labelling techniques for the detection of active diazotrophs

Investigating active participants in the fixation of dinitrogen gas is vital as N is often a limiting factor for primary production. Biological nitrogen fixation is performed by a diverse guild of bacteria and archaea (diazotrophs), which can be free-living or symbionts. Free-living diazotrophs are widely distributed in the environment, yet our knowledge about their identity and ecophysiology is still limited. A major challenge in investigating this guild is inferring activity from genetic data as this process is highly regulated. To address this challenge, we evaluated and improved several 15 N-based methods for detecting N2 fixation activity (with a focus on soil samples) and studying active diazotrophs. We compared the acetylene reduction assay and the 15 N2 tracer method and demonstrated that the latter is more sensitive in samples with low activity. Additionally, tracing 15 N into microbial RNA provides much higher sensitivity compared to bulk soil analysis. Active soil diazotrophs were identified with a 15 N-RNA-SIP approach optimized for environmental samples and benchmarked to 15 N-DNA-SIP. Lastly, we investigated the feasibility of using SIP-Raman microspectroscopy for detecting 15 N-labelled cells. Taken together, these tools allow identifying and investigating active free-living diazotrophs in a highly sensitive manner in diverse environments, from bulk to the single-cell level.

Culture-Free Detection of Crop Pathogens at the Single-Cell Level by Micro-Raman Spectroscopy

The rapid and sensitive identification of invasive plant pathogens has important applications in biotechnology, plant quarantine, and food security. Current methods are far too time-consuming and need a pre-enrichment period ranging from hours to days. Here, a micro-Raman spectroscopy-based bioassay for culture-free pathogen quarantine inspection at the single cell level within 40 min is presented. The application of this approach can readily and specifically detect plant pathogens Burkholderia gladioli pv. alliicola and Erwinia chrysanthemi that are closely related pathogenically. Furthermore, the single-bacterium detection was able to discriminate them from a reference Raman spectral library including multiple quarantine-relevant pathogens with broad host ranges and an array of pathogenic variants. To show the usefulness of this assay, Burkholderia gladioli pv. alliicola and Erwinia chrysanthemi are detected at single-bacterium level in plant tissue lesions without pre-enrichment. The results are confirmed by the plate-counting method and a genetic molecular approach, which display comparable recognition ratios to the Raman spectroscopy-based bioassay. The results represent a critical step toward the use of micro-Raman spectroscopy in rapid and culture-free discrimination of quarantine relevant plant pathogens.

Novel approaches in function-driven single-cell genomics

Deeper sequencing and improved bioinformatics in conjunction with single-cell and metagenomic approaches continue to illuminate undercharacterized environmental microbial communities. This has propelled the 'who is there, and what might they be doing' paradigm to the uncultivated and has already radically changed the topology of the tree of life and provided key insights into the microbial contribution to biogeochemistry. While characterization of 'who' based on marker genes can describe a large fraction of the community, answering 'what are they doing' remains the elusive pinnacle for microbiology. Function-driven single-cell genomics provides a solution by using a function-based screen to subsample complex microbial communities in a targeted manner for the isolation and genome sequencing of single cells. This enables single-cell sequencing to be focused on cells with specific phenotypic or metabolic characteristics of interest. Recovered genomes are conclusively implicated for both encoding and exhibiting the feature of interest, improving downstream annotation and revealing activity levels within that environment. This emerging approach has already improved our understanding of microbial community functioning and facilitated the experimental analysis of uncharacterized gene product space. Here we provide a comprehensive review of strategies that have been applied for function-driven single-cell genomics and the future directions we envision.

Quantitative detection of isotopically enrichedE. colicells by SERS

It is clear that investigating how bacterial cells work by analysing their functional roles in microbial communities is very important in environmental, clinical and industrial microbiology. The benefits of linking genes to their respective functions include the reliable identification of the causative agents of various diseases, which would permit appropriate and timely treatment in healthcare systems. In industrial and municipal wastewater treatment and management, such knowledge may allow for the manipulation of microbial communities, such as through bioaugmentation, in order to improve the efficiency and effectiveness of bioremediation processes. Stable isotope probing coupled with identification techniques has emerged to be a potentially reliable tool for the discrimination, identification and characterization of bacteria at community and single cell levels, knowledge which can be utilized to link microbially mediated bioprocesses to phylogeny. Development of the surface-enhanced Raman scattering (SERS) technique offers an exciting alternative to the Raman and Fourier-transform infrared spectroscopic techniques in understanding the metabolic processes of microorganismsin situ. SERS employing Ag and Au nanoparticles can significantly enhance the Raman signal, making it an exciting candidate for the analysis of the cellular components of microorganisms. In this study,Escherichia colicells were cultivated in minimal medium containing different ratios of¹²C/¹³C glucose and/or¹⁴N/¹⁵N ammonium chloride as the only carbon and nitrogen sources respectively, with the overall final concentrations of these substrates being constant. After growth, theE. colicells were analyzed with SERS employing anin situsynthesis of Ag nanoparticles. This novel investigation of the SERS spectral data with multivariate chemometrics demonstrated clear clusters which could be correlated to the SERS spectral shifts of biomolecules from cells grown and hence labelled with¹³C and¹⁵N atoms. These shifts reflect the isotopic content of the bacteria and quantification of the isotope levels could be established using chemometrics based on partial least squares regression.

New Technologies for Rapid Bacterial Identification and Antibiotic Resistance Profiling

Conventional approaches to bacterial identification and drug susceptibility testing typically rely on culture-based approaches that take 2 to 7 days to return results. The long turnaround times contribute to the spread of infectious disease, negative patient outcomes, and the misuse of antibiotics that can contribute to antibiotic resistance. To provide new solutions enabling faster bacterial analysis, a variety of approaches are under development that leverage single-cell analysis, microfluidic concentration and detection strategies, and ultrasensitive readout mechanisms. This review discusses recent advances in this area and the potential of new technologies to enable more effective management of infectious disease.

Single-cell level methods for studying the effect of antibiotics on bacteria during infection

Considerable evidence about phenotypic heterogeneity among bacteria during infection has accumulated during recent years. This heterogeneity has to be considered if the mechanisms of infection and antibiotic action are to be understood, so we need to implement existing and find novel methods to monitor the effects of antibiotics on bacteria at the single-cell level. This review provides an overview of methods by which this aim can be achieved. Fluorescence label-based methods and Raman scattering as a label-free approach are discussed in particular detail. Other label-free methods that can provide single-cell level information, such as impedance spectroscopy and surface plasmon resonance, are briefly summarized. The advantages and disadvantages of these different methods are discussed in light of a challenging in vivo environment.

Single cell stable isotope probing in microbiology using Raman microspectroscopy

Microbial communities are essential for most ecosystem processes and interact in highly complex ways with virtually all eukaryotes. Thus, a detailed understanding of the function of such communities is a fundamental prerequisite for microbial ecologists, applied microbiologists and microbiome researchers. Using single cell Raman microspectroscopy, biochemical fingerprints of individual microbial cells can be obtained in an externally label-free and non-destructive manner. If combined with stable isotope probing (SIP), Raman spectroscopy can directly reveal functions of single microorganisms in their natural habitat. This review provides an update on various SIP-approaches suitable for combination with different Raman scattering techniques and illustrates how single cell Raman SIP can be directly combined with the omics-centric analysis pipelines to investigate microbial communities.

Raman activated cell sorting

Single cell Raman spectra (SCRS) are intrinsic biochemical profiles and 'chemical images' of single cells which can be used to characterise phenotypic changes, physiological states and functions of cells. On the base of SCRS, Raman activated cell sorting (RACS) provides a label-free cell sorting approach, which can link single cells to their chemical or phenotypic profiles. Overcoming naturally weak Raman signals, establishing Raman biomarker as sorting criteria to RACS and improving specific sorting technology are three challenges of developing RACS. Advances on Raman spectroscopy such as stimulated Raman scattering (SRS) and pre-screening helped to increase RACS sorting speed. Entire SCRS can be characterised using pattern recognition methods, and specific Raman bands can be extracted as biomarkers for RACS. Recent advances on cell sorting technologies based on microfluidic device and surface-ejection enable accurate and reliable single cell sorting from complex samples. A high throughput RACS will be achievable in near future by integrating fast Raman detection system such as SRS with microfluidic RACS and Raman activated cell ejection (RACE).

Surface-Enhanced Raman Spectroscopy for Identification of Heavy Metal Arsenic(V)-Mediated Enhancing Effect on Antibiotic Resistance

Bacterial antibiotic resistance poses a threat to global public health. Restricted usage of antibiotics does not necessarily prevent its continued emergence. Rapid and sensitive screening of triggers, in addition to antibiotic, and exploring the underlying mechanism are still major challenges. Herein, by developing a homogeneous vacuum filtration-based bacterial sample fabrication enabling high surface-enhanced Raman scattering (SERS) reproducibility across multiple bacterial samples and negating interfering spectral variations from inhomogeneous sample geometry and SERS enhancement, SERS was employed to study heavy metal arsenic [As(V)]-mediated antibiotic resistance in a robust, sensitive, and rapid fashion. Independent and robust spectral changes representing phenotypic bacterial responses, combined with multivariate analysis, clearly identified that As(V) enhanced antibiotic resistance to tetracycline (Tet). Similar spectral alteration profile to As(V) and Tet indicated that cross-resistance, whereby As(V)-induced bacterial resistance simultaneously blocked Tet action, could account for the enhanced resistance. The sensitive, robust, and rich phenotypic profile provided by SERS, combined with additional advantages in imposing no need to cultivate bacteria and single-cell sensitivity, can be further exploited to evaluate resistance-intervening factors in real microbiota.

Tracing amino acid exchange during host-pathogen interaction by combined stable-isotope time-resolved Raman spectral imaging

This study investigates the temporal and spatial interchange of the aromatic amino acid phenylalanine (Phe) between human retinal pigment epithelial cell line (ARPE-19) and tachyzoites of the apicomplexan protozoan parasite Toxoplasma gondii (T. gondii). Stable isotope labelling by amino acids in cell culture (SILAC) is combined with Raman micro-spectroscopy to selectively monitor the incorporation of deuterium-labelled Phe into proteins in individual live tachyzoites. Our results show a very rapid uptake of l-Phe(D8) by the intracellular growing parasite. T. gondii tachyzoites are capable of extracting l-Phe(D8) from host cells as soon as it invades the cell. l-Phe(D8) from the host cell completely replaces the l-Phe within T. gondii tachyzoites 7-9 hours after infection. A quantitative model based on Raman spectra allowed an estimation of the exchange rate of Phe as 0.5-1.6 × 10(4) molecules/s. On the other hand, extracellular tachyzoites were not able to consume l-Phe(D8) after 24 hours of infection. These findings further our understanding of the amino acid trafficking between host cells and this strictly intracellular parasite. In particular, this study highlights new aspects of the metabolism of amino acid Phe operative during the interaction between T. gondii and its host cell.