Perspective on Surface-Enhanced Raman Spectroscopic Investigation of Microbial World

Aerobic Anoxygenic Phototrophic Bacteria in the Marine Environments Revealed by Raman/Fluorescence-Guided Single-Cell Sorting and Targeted Metagenomics

Aerobic anoxygenic phototrophic bacteria (AAPB) contribute profoundly to the global carbon cycle. However, most AAPB in marine environments are uncultured and at low abundance, hampering the recognition of their functions and molecular mechanisms. In this study, we developed a new culture-independent method to identify and sort AAPB using single-cell Raman/fluorescence spectroscopy. Characteristic Raman and fluorescent bands specific to bacteriochlorophyll a (Bchl a) in AAPB were determined by comparing multiple known AAPB with non-AAPB isolates. Using these spectroscopic biomarkers, AAPB in coastal seawater, pelagic seawater, and hydrothermal sediment samples were screened, sorted, and sequenced. 16S rRNA gene analysis and functional gene annotations of sorted cells revealed novel AAPB members and functional genes, including one species belonging to the genus Sphingomonas, two genera affiliated to classes Betaproteobacteria and Gammaproteobacteria, and function genes bchCDIX, pucC2, and pufL related to Bchl a biosynthesis and photosynthetic reaction center assembly. Metagenome-assembled genomes (MAGs) of sorted cells from pelagic seawater and deep-sea hydrothermal sediment belonged to Erythrobacter sanguineus that was considered as an AAPB and genus Sphingomonas, respectively. Moreover, multiple photosynthesis-related genes were annotated in both MAGs, and comparative genomic analysis revealed several exclusive genes involved in amino acid and inorganic ion metabolism and transport. This study employed a new single-cell spectroscopy method to detect AAPB, not only broadening the taxonomic and genetic contents of AAPB in marine environments but also revealing their genetic mechanisms at the single-genomic level.

Illuminating the Tiny World: A Navigation Guide for Proper Raman Studies on Microorganisms

Raman spectroscopy is an emerging method for the identification of bacteria. Nevertheless, a lot of different parameters need to be considered to establish a reliable database capable of identifying real-world samples such as medical or environmental probes. In this review, the establishment of such reliable databases with the proper design in microbiological Raman studies is demonstrated, shining a light into all the parts that require attention. Aspects such as the strain selection, sample preparation and isolation requirements, the phenotypic influence, measurement strategies, as well as the statistical approaches for discrimination of bacteria, are presented. Furthermore, the influence of these aspects on spectra quality, result accuracy, and read-out are discussed. The aim of this review is to serve as a guide for the design of microbiological Raman studies that can support the establishment of this method in different fields.

Label-Free Surface-Enhanced Raman Scattering Detection of Fire Blight Pathogen Using a Pathogen-Specific Bacteriophage

Fire blight is one of the most devastating plant diseases, causing severe social and economic problems. Herein, we report a novel method based on label-free surface-enhanced Raman scattering (SERS) combined with an Erwinia amylovora-specific bacteriophage that allows detecting efficiently fire blight bacteria E. amylovora for the first time. To achieve the highest SERS signals for E. amylovora, we synthesized and compared plasmonic nanoparticles (PNPs) with different sizes, i.e., bimetallic gold core-silver shell nanoparticles (Au@AgNPs) and monometallic gold nanoparticles (AuNPs) and utilized the coffee-ring effect for the self-assembly of PNPs and enrichment of fire blight bacteria. Furthermore, we investigated the changes in the SERS spectra of E. amylovora after incubation with an E. amylovora-specific bacteriophage, and we found considerable differences in the SERS signals as a function of the bacteriophage incubation time. The results indicate that our bacteriophage-based label-free SERS analysis can specifically detect E. amylovora without the need for peak assignment on the SERS spectra but simply by monitoring the changes in the SERS signals over time. Therefore, our facile method holds great potential for the label-free detection of pathogenic bacteria and the investigation of viral-bacterial interactions.

Metabolite-Mediated Bacterial Antibiotic Resistance Revealed by Surface-Enhanced Raman Spectroscopy

A prompt on-site, real-time method to detect bacterial antibiotic resistance is crucial for controlling the spread of resistance. Herein, we report the use of surface-enhanced Raman spectroscopy (SERS) for the monitoring of bioactive metabolites produced by ampicillin-resistant Pseudomonas aeruginosa strains and identification of mechanisms underlying antibiotic resistance. The results indicate that the blue-green pigment pyocyanin (PYO) dominates the metabolite signals and is significantly enhanced upon exposure to subminimal inhibitory concentrations of ampicillin. PYO accumulates during exponential growth and subsequently either diffuses into the culture medium or is consumed in response to nutrient deprivation. The SERS spectra further reveal that the production of some intermediate substances such as polysaccharides and amino acids is minimally impacted and that nutrient consumption remains consistent. Moreover, the intensity changes and peak shifts observed in the SERS spectra of non-PYO-producing ampicillin-susceptible Escherichia coli demonstrate that exogenously added PYO enhances E. coli tolerance to ampicillin to some extent. These results indicate that PYO mediates antibiotic resistance not only in the parent species but also in cocultured bacterial strains. The metabolic SERS signal provides new insight regarding antibiotic resistance with promising applications for both environmental monitoring and rapid clinical detection.

Nano-Biotechnology for Bacteria Identification and Potent Anti-bacterial Properties: A Review of Current State of the Art

Sepsis is a critical disease caused by the abrupt increase of bacteria in human blood, which subsequently causes a cytokine storm. Early identification of bacteria is critical to treating a patient with proper antibiotics to avoid sepsis. However, conventional culture-based identification takes a long time. Polymerase chain reaction (PCR) is not so successful because of the complexity and similarity in the genome sequence of some bacterial species, making it difficult to design primers and thus less suitable for rapid bacterial identification. To address these issues, several new technologies have been developed. Recent advances in nanotechnology have shown great potential for fast and accurate bacterial identification. The most promising strategy in nanotechnology involves the use of nanoparticles, which has led to the advancement of highly specific and sensitive biosensors capable of detecting and identifying bacteria even at low concentrations in very little time. The primary drawback of conventional antibiotics is the potential for antimicrobial resistance, which can lead to the development of superbacteria, making them difficult to treat. The incorporation of diverse nanomaterials and designs of nanomaterials has been utilized to kill bacteria efficiently. Nanomaterials with distinct physicochemical properties, such as optical and magnetic properties, including plasmonic and magnetic nanoparticles, have been extensively studied for their potential to efficiently kill bacteria. In this review, we are emphasizing the recent advances in nano-biotechnologies for bacterial identification and anti-bacterial properties. The basic principles of new technologies, as well as their future challenges, have been discussed.

Sensing of Antibiotic-Bacteria Interactions

Sensing of antibiotic-bacteria interactions is an important area of research that has gained significant attention in recent years. Antibiotic resistance is a major public health concern, and it is essential to develop new strategies for detecting and monitoring bacterial responses to antibiotics in order to maintain effective antibiotic development and antibacterial treatment. This review summarizes recent advances in sensing strategies for antibiotic-bacteria interactions, which are divided into two main parts: studies on the mechanism of action for sensitive bacteria and interrogation of the defense mechanisms for resistant ones. In conclusion, this review provides an overview of the present research landscape concerning antibiotic-bacteria interactions, emphasizing the potential for method adaptation and the integration of machine learning techniques in data analysis, which could potentially lead to a transformative impact on mechanistic studies within the field.

Antimicrobial Agent against Methicillin-Resistant Staphylococcus aureus Biofilm Monitored Using Raman Spectroscopy

The prevalence of antimicrobial-resistant bacteria has become a major challenge worldwide. Methicillin-resistant Staphylococcus aureus (MRSA)-a leading cause of infections-forms biofilms on polymeric medical devices and implants, increasing their resistance to antibiotics. Antibiotic administration before biofilm formation is crucial. Raman spectroscopy was used to assess MRSA biofilm development on solid culture media from 0 to 48 h. Biofilm formation was monitored by measuring DNA/RNA-associated Raman peaks and protein/lipid-associated peaks. The search for an antimicrobial agent against MRSA biofilm revealed that Eugenol was a promising candidate as it showed significant potential for breaking down biofilm. Eugenol was applied at different times to test the optimal time for inhibiting MRSA biofilms, and the Raman spectrum showed that the first 5 h of biofilm formation was the most antibiotic-sensitive time. This study investigated the performance of Raman spectroscopy coupled with principal component analysis (PCA) to identify planktonic bacteria from biofilm conglomerates. Raman analysis, microscopic observation, and quantification of the biofilm growth curve indicated early adhesion from 5 to 10 h of the incubation time. Therefore, Raman spectroscopy can help in monitoring biofilm formation on a solid culture medium and performing rapid antibiofilm assessments with new antibiotics during the early stages of the procedure.

Recent Progress of Surface-Enhanced Raman Spectroscopy for Bacteria Detection

There are various pathogenic bacteria in the surrounding living environment, which not only pose a great threat to human health but also bring huge losses to economic development. Conventional methods for bacteria detection are usually time-consuming, complicated and labor-intensive, and cannot meet the growing demands for on-site and rapid analyses. Sensitive, rapid and effective methods for pathogenic bacteria detection are necessary for environmental monitoring, food safety and infectious bacteria diagnosis. Recently, benefiting from its advantages of rapidity and high sensitivity, surface-enhanced Raman spectroscopy (SERS) has attracted significant attention in the field of bacteria detection and identification as well as drug susceptibility testing. Here, we comprehensively reviewed the latest advances in SERS technology in the field of bacteria analysis. Firstly, the mechanism of SERS detection and the fabrication of the SERS substrate were briefly introduced. Secondly, the label-free SERS applied for the identification of bacteria species was summarized in detail. Thirdly, various SERS tags for the high-sensitivity detection of bacteria were also discussed. Moreover, we emphasized the application prospects of microfluidic SERS chips in antimicrobial susceptibility testing (AST). In the end, we gave an outlook on the future development and trends of SERS in point-of-care diagnoses of bacterial infections.

Investigation of the Influence of Stress on Label-Free Bacterial Surface-Enhanced Raman Spectra

Label-free surface-enhanced Raman spectroscopy (SERS) has been proposed as a promising bacterial detection technique. However, the quality of the collected bacterial spectra can be affected by the time between sample acquisition and the SERS measurement. This study evaluated how storage stress stimuli influence the label-free SERS spectra of Pseudomonas syringae samples stored in phosphate buffered saline. The results indicate that when faced with nutrient limitations and changes in osmatic pressure, samples at room temperature (25 °C) exhibit more significant spectral changes than those stored at cold temperature (4 °C). At higher temperatures, bacterial communities secrete extracellular biomolecules that induce programmed cell death and result in increases in the supernatant SERS signals. Surviving cells consume cellular components to support their metabolism, thus leading to measurable declines in cell SERS intensity. Two-dimensional correlation spectroscopy analysis suggests that cellular component signatures decline sequentially in the following order: proteins, nucleic acids, and lipids. Extracellular nucleic acids, proteins, and carbohydrates are secreted in turn. After subtracting the SERS changes resulting from storage, we evaluated bacterial response to viral infection. P. syringae SERS profile changes enable accurate bacteriophage Phi6 quantification over the range of 10⁴-10¹⁰ PFU/mL. The results indicate that storage conditions impact bacterial label-free SERS signals and that such influences need to be accounted for and if possible avoided when detecting bacteria or evaluating bacterial response to stress stimuli.

SERS-based antibiotic susceptibility testing: Towards point-of-care clinical diagnosis

Emerging antibiotic resistant bacteria constitute one of the biggest threats to public health. Surface-enhanced Raman scattering (SERS) is highly promising for detecting such bacteria and for antibiotic susceptibility testing (AST). SERS is fast, non-destructive (can probe living cells) and it is technologically flexible (readily integrated with robotics and machine learning algorithms). However, in order to integrate into efficient point-of-care (PoC) devices and to effectively replace the current culture-based methods, it needs to overcome the challenges of reliability, cost and complexity. Recently, significant progress has been made with the emergence of both new questions and new promising directions of research and technological development. This article brings together insights from several representative SERS-based AST studies and approaches oriented towards clinical PoC biosensing. It aims to serve as a reference source that can guide progress towards PoC routines for identifying antibiotic resistant pathogens. In turn, such identification would help to trace the origin of sporadic infections, in order to prevent outbreaks and to design effective medical treatment and preventive procedures.

Ag NP-filter paper based SERS sensor coupled with multivariate analysis for rapid identification of bacteria

Rapid and accurate identification of bacteria is essential to ensure food safety and prevent pathogenic bacterial infection. In this study, a highly efficient method was established for accurately identifying bacterial species by applying Ag NP-filter paper based Surface enhanced Raman spectroscopy (SERS) analysis and Partial Least Squares-Discriminant Analysis (PLS-DA) statistical methods. The flexible Ag NP filter paper substrate with high sensitivity and uniformity was prepared by a facile and low-cost silver mirror reaction at room temperature, which exhibited desirable SERS activity in bacteria detection. Furthermore, PLS-DA was successfully employed to distinguish SERS spectra from S. aureus CMCC 26003, E. faecalis ATCC29212 and L. monocytogenes ATCC 19115 with a sensitivity of 93.3-100%, specificity of 96.7-97%, and overall predicting accuracy of 95.8%. This exploratory study demonstrates that a Ag NP-filter paper based SERS sensor coupled with PLS-DA has great potential for rapid and effective detection and identification of bacteria.

Surface-enhanced Raman spectroscopy enabled evaluation of bacterial inactivation

An improved understanding of bacterial inactivation mechanisms will provide useful insights for infectious disease control and prevention. We evaluated bacterial response to several inactivation methods using surface-enhanced Raman spectroscopy (SERS). The results indicate that changes in the SERS signal are highly related to cellular disruption and that cellular changes arising after cell inactivation cannot be ignored. The membrane integrity of heat and the combination of UV₂₅₄ and free chlorine (UV₂₅₄/chlorine) treated Pseudomonas syringae (P. syringae) cells were severely disrupted, leading to significantly increased peak intensities. Conversely, ethanol treated bacteria exhibited intact cell morphologies and the SERS spectra remained virtually unchanged. On the basis of time dependent SERS signals, we extracted dominant SERS patterns. Peaks related to nucleic acids accounted for the main changes observed during heat, UV₂₅₄, and UV₂₅₄/chlorine treatment, likely due to their outward diffusion from the cell cytoplasm. For free chlorine treated P. syringae, carbohydrates and proteins on the cell membrane were denatured or lost, resulting in a decrease in related peak intensities. The nucleobases were likely oxidized when treated with UV₂₅₄ and chlorine, thus leading to shifts in the related peaks. The generality of the method was verified using two additional bacterial strains: Escherichia coli and Bacillus subtilis as well as in different water matrices. The results suggest that SERS spectral analysis is a promising means to examine bacterial stress response at the molecular level and has applicability in diverse environmental implementations.

Assessing the effect of different pH maintenance situations on bacterial SERS spectra

Phenotyping of bacteria with vibrational spectroscopy has caught much attention in bacteria-related research. It is known that many factors could affect this process. Among them, solution pH maintenance is crucial, yet its impact on the bacterial SERS spectra is surprisingly neglected. In this work, we focused on two situations related to pH maintenance: the effect of the same buffer on the SERS spectra of bacteria under different pH values, and the influence of different buffers on the SERS spectra of bacteria under the same pH value. Specifically, Britton-Robison (BR) buffer was used to evaluate the effect of pH value on bacteria SERS spectra thanks to its wide pH range. Four different buffers, namely BR buffer, acetate buffer, phosphate buffer, and carbonate buffer, were used to illustrate the impact of buffer types on SERS spectra of bacteria. The results showed that the intensity and number of characteristic peaks of the SERS spectra of Gram-negative (G -) bacteria changed more significantly than Gram-positive (G +) bacteria with the change of pH value. Furthermore, compared with phosphate buffer and carbonate buffer, BR buffer could bring more characteristic SERS bands with better reproducibility, but slightly inferior to acetate buffer. In conclusion, the influence of the pH and types of the buffer on the SERS spectra of bacteria are worthy of further discussion.

Research on the Comprehensive Evaluation Method for the Automatic Recognition of Raman Spectrum under Multidimensional Constraint

Raman spectrum contains abundant substance information with fingerprint characteristics. However, due to the huge variety of substances and their complex characteristic information, it is difficult to recognize the Raman spectrum accurately. Starting from dimensions like the Raman shift, the relative peak intensity, and the overall hit ratio of characteristic peaks, we extracted and recognized the characteristics in the Raman spectrum and analyzed these characteristics from local and global perspectives and then proposed a comprehensive evaluation method for the recognition of Raman spectrum on the basis of the data fusion of the recognition results under multidimensional constraint. Based on the common spectrum database of the normal Raman and surface-enhanced Raman of thousands of substances, we analyzed the performance of the evaluation method. It shows that even for the identification of spectra from instruments of low technical specifications, the automatic recognition rate of the sample can reach 98% and above, a great improvement compared with that of the common identification algorithms, which proves the effectiveness of the comprehensive evaluation method under multidimensional constraint.

Boosting bacteria differentiation efficiency with multidimensional surface-enhanced Raman scattering: the example of Bacillus cereus

Surface-enhanced Raman scattering (SERS) is a powerful tool for constructing biomolecular fingerprints, which play a vital role in differentiation of bacteria. Due to the rather subtle differences in the SERS spectra among different bacteria, artificial intelligence is usually adopted and enormous amounts of spectral data are required to improve the differentiation efficiency. However, in many cases, large volume data acquisition on bacteria is not only technical difficult but labour intensive. It is known that surface modification of SERS nanomaterials can bring additional dimensionality (difference) of the SERS fingerprints. Here in this work, we show that the concept could be used to improve the bacteria differentiation efficiency. Ag NPs were modified with 11-mercaptoundecanoic acid, 11-mercapto-1-undecanol, and 1-dodecanethiol to provide additional dimensionality. The modified NPs then were mixed with cell lysate from different strains of Bacillus cereus (B. cereus). Even by applying a simple PCA process to the resulting SERS spectra data, all the three modified Ag NPs showed superior differentiation results compared with bare Ag NPs, which could only separate Staphylococcus aureus (S. aureus) and B. cereus. It is believed that the multidimensional SERS could find great potential in bacteria differentiation.

Phenotyping Bacteria through a Black-Box Approach: Amplifying Surface-Enhanced Raman Spectroscopy Spectral Differences among Bacteria by Inputting Appropriate Environmental Stress

Surface-enhanced Raman spectroscopy (SERS) stands out in the field of microbial analysis due to its rich molecular information, fast analysis speed, and high sensitivity. However, achieving strain-level differentiation is still challenging because numerous bacterial species inevitably have very similar SERS profiles. Here, a method inspired by the black-box theory was proposed to boost the spectral differences, where the undifferentiated bacteria was considered as a type of black-box, external environmental stress was used as the input, and the SERS spectra of bacteria exposed to the same stress was output. For proof of the concept, three types of environmental stress were explored, i.e., ethanol, ultraviolet light (UV), and ultrasound. Enterococcus faecalis (E. faecalis) and three types of Escherichia coli (E. coli) were all subjected to the stimuli (stress) before SERS measurement. Then the collected spectra were processed only by simple principal component analysis (PCA) to achieve differentiation. The results showed that appropriate stress was beneficial to increase the differences in bacterial SERS spectra. When sonication at 490 W for 60 s was used as the input, the optimal differentiation of bacteria at the species (E. faecalis and E. coli) and strain-level (three E. coli) can be achieved.

Microfluidics as an Emerging Platform for Exploring Soil Environmental Processes: A Critical Review

Investigating environmental processes, especially those occurring in soils, calls for innovative and multidisciplinary technologies that can provide insights at the microscale. The heterogeneity, opacity, and dynamics make the soil a "black box" where interactions and processes are elusive. Recently, microfluidics has emerged as a powerful research platform and experimental tool which can create artificial soil micromodels, enabling exploring soil processes on a chip. Micro/nanofabricated microfluidic devices can mimic some of the key features of soil with highly controlled physical and chemical microenvironments at the scale of pores, aggregates, and microbes. The combination of various techniques makes microfluidics an integrated approach for observation, reaction, analysis, and characterization. In this review, we systematically summarize the emerging applications of microfluidic soil platforms, from investigating soil interfacial processes and soil microbial processes to soil analysis and high-throughput screening. We highlight how innovative microfluidic devices are used to provide new insights into soil processes, mechanisms, and effects at the microscale, which contribute to an integrated interrogation of the soil systems across different scales. Critical discussions of the practical limitations of microfluidic soil platforms and perspectives of future research directions are summarized. We envisage that microfluidics will represent the technological advances toward microscopic, controllable, and in situ soil research.

Recent advancement in nano-optical strategies for detection of pathogenic bacteria and their metabolites in food safety

Pathogenic bacteria and their metabolites are the leading risk factor in food safety and are one of the major threats to human health because of the capability of triggering diseases with high morbidity and mortality. Nano-optical sensors for bacteria sensing have been greatly explored with the emergence of nanotechnology and artificial intelligence. In addition, with the rapid development of cross fusion technology, other technologies integrated nano-optical sensors show great potential in bacterial and their metabolites sensing. This review focus on nano-optical strategies for bacteria and their metabolites sensing in the field of food safety; based on surface-enhanced Raman scattering (SERS), fluorescence, and colorimetric biosensors, and their integration with the microfluidic platform, electrochemical platform, and nucleic acid amplification platform in the recent three years. Compared with the traditional techniques, nano optical-based sensors have greatly improved the sensitivity with reduced detection time and cost. However, challenges remain for the simple fabrication of biosensors and their practical application in complex matrices. Thus, bringing out improvements or novelty in the pretreatment methods will be a trend in the upcoming future.

A microfluidic microwell device operated by the automated microfluidic control system for surface-enhanced Raman scattering-based antimicrobial susceptibility testing

Bloodstream infection (BSI) is a serious public health issue worldwide. Timely and effective antibiotics for controlling infection are crucial towards patient outcomes. However, the current culture-based methods of identifying bacteria and antimicrobial susceptibility testing (AST) remain labor-intensive and time-consuming, and are unable to provide early support to physicians in critical hours. To improve the effectiveness of early antibiotic therapy, Surface-enhanced Raman scattering (SERS) technology, has been used in bacterial detection and AST based on its high specificity and label-free features. To simplify sample preparation steps in SERS-AST, we proposed an automated microfluidic control system to integrate all required procedures into a single device. Our preliminary results demonstrated the system can achieve on-chip reagent replacement, bacteria trapping, and buffer exchange. Finally, in-situ SERS-AST was performed within 3.5 h by loading isolates of ampicilin susceptible and resistant E. coli and clear discrimination of two strains under antibiotic treatment was demonstrated. Overall, our system can standardize and simplify the SERS-AST protocol and implicate parallel bacterial detection. This prototypical integration demonstrates timely microbiological support to optimize early antibiotic therapy for fighting bacteremia.

The rationality of using coreshell nanoparticles with embedded internal standards for SERS quantitative analysis based glycerol-assisted 3D hotspots platform

Surface enhanced Raman spectroscopy (SERS) is a promising sensing technique that can provide unique chemical and structural fingerprint information, but gaining reliable SERS quantitative data with high sensitivity and stability still remains a challenge. Although using a molecule as an internal standard (IS) can improve the SERS quantitative capability, the reliability and SERS measuring conditions for signal fluctuations during calibration based on IS are yet to be explored when the embedded IS molecules and target objects are located in different environments. Herein, a 3D hotspot matrix SERS platform based on Au@4-MPy@AgNPs was constructed in water with the assistance of glycerol and the dynamic signal changes from the IS, i.e. 4-Mpy, and target molecules were monitored during the process of evaporation with high sensitivity and stability. In contrast to the traditional water-dispersed drying film system, the variation trends of IS and target molecules were consistent in the glycerol-assisted liquid film protection system. Therefore, it is reasonable to calibrate the signal fluctuation by utilizing the embedded IS based on the construction strategy of a glycerol-assisted 3D hotspot platform. This work demonstrates a rational, reliable and precise SERS quantitative technique for testing analyte concentrations in practical systems and has great application prospects in the field of analytical chemistry.

3D hotspots matrix SERS platform in water with the assistance of 2.5% v/v glycerol has been constructed and then used in investigating the rationality of using core–shell nanoparticles with embedded internal standards for SERS quantitative analysis.

Potential of indigenous crop microbiomes for sustainable agriculture

The intimate interactions of indigenous crops with their associated microbiomes during long-term co-evolution strengthen the capacity and flexibility of crops to cope with biotic and abiotic stresses. This represents a promising untapped field for searching novel tools to sustainably increase crop productivity. However, the current capability of harnessing the power of indigenous crop microbiomes for sustainable crop production is limited due to low efficiency of separating the targeted functional microbes. Here, we highlight the potential benefits and existing challenges of utilizing indigenous crop microbiomes to reduce agrochemical inputs and increase crop resistance to biotic and abiotic stresses. We propose a framework using Raman-spectroscopy-based single-cell-sorting technology combined with a synthetic community approach to design and optimize a functionally reliable 'beneficial biome' under controlled conditions. This framework will offer opportunities for sustainable agriculture and provide a new direction for future studies.

Recent Advances in the Detection of Antibiotic and Multi-Drug Resistant Salmonella: An Update

Antibiotic and multi-drug resistant (MDR) Salmonella poses a significant threat to public health due to its ability to colonize animals (cold and warm-blooded) and contaminate freshwater supplies. Monitoring antibiotic resistant Salmonella is traditionally costly, involving the application of phenotypic and genotypic tests over several days. However, with the introduction of cheaper semi-automated devices in the last decade, strain detection and identification times have significantly fallen. This, in turn, has led to efficiently regulated food production systems and further reductions in food safety hazards. This review highlights current and emerging technologies used in the detection of antibiotic resistant and MDR Salmonella.

Enhancing the Activity of Silver Nanowire Membranes by Electrochemical Cyclic Voltammetry as Highly Sensitive Flexible SERS Substrate for On-Site Analysis

The development of high-quality flexible surface-enhanced Raman spectroscopy (SERS) substrates is crucial for developing rapid SERS analysis in situ. Silver nanowire membranes as novel flexible substrates could benefit from the high collection efficiency of analytes by wrapping complex surfaces or wiping the surfaces of samples. However, their low SERS performance impedes further applications of silver nanowire membranes in analyte detection. Herein, we report an ultra-high-sensitivity silver nanowire membrane synthesized by a simple and time-saving cyclic voltammetry (CV) method. After CV treatment, a part of the silver nanowires on the silver nanowire membrane turned into small nanoparticles and nanorods. This nanostructure’s reconstitution increased the analytical enhancement factor of silver nanowire membranes by 14.4 times. Scanning and transmission electron microscopy, UV-vis spectroscopy, X-ray diffraction, and X-ray photoelectron spectroscopy were employed to investigate the transformation in the membrane nanostructure. The CV-treated substrates exhibited high surface-enhanced Raman activity and good temporal stability. The limits of detection (LODs) for p-aminothiophenol, crystal violet, tetramethylthiuram disulfide, sodium perchlorate, malachite green, fluoranthene, and potassium nitrate are 3.7 × 10⁻¹² M, 5.1 × 10⁻¹¹ M, 5.4 × 10⁻¹¹ M, 6.3 × 10⁻⁹ M, 0.00693 ng, 0.0810 ng, and 0.0273 ng on this substrate, respectively. Additionally, the developed substrate is feasible for the detection of crystal violet in real samples. These results certify that CV-treated substrates possess broad application prospects in on-site SERS analysis.

Recent progress of surface-enhanced Raman spectroscopy for subcellular compartment analysis

Organelles are involved in many cell life activities, and their metabolic or functional disorders are closely related to apoptosis, neurodegenerative diseases, cardiovascular diseases, and the development and metastasis of cancers. The explorations of subcellular structures, microenvironments, and their abnormal conditions are conducive to a deeper understanding of many pathological mechanisms, which are expected to achieve the early diagnosis and the effective therapy of diseases. Organelles are also the targeted locations of drugs, and they play significant roles in many targeting therapeutic strategies. Surface-enhanced Raman spectroscopy (SERS) is a powerful analytical tool that can provide the molecular fingerprint information of subcellular compartments and the real-time cellular dynamics in a non-invasive and non-destructive way. This review aims to summarize the recent advances of SERS studies on subcellular compartments, including five parts. The introductions of SERS and subcellular compartments are given. SERS is promising in subcellular compartment studies due to its molecular specificity and high sensitivity, and both of which highly match the high demands of cellular/subcellular investigations. Intracellular SERS is mainly cataloged as the labeling and label-free methods. For subcellular targeted detections and therapies, how to internalize plasmonic nanoparticles or nanostructure in the target locations is a key point. The subcellular compartment SERS detections, SERS measurements of isolated organelles, investigations of therapeutic mechanisms from subcellular compartments and microenvironments, and integration of SERS diagnosis and treatment are sequentially presented. A perspective view of the subcellular SERS studies is discussed from six aspects. This review provides a comprehensive overview of SERS applications in subcellular compartment researches, which will be a useful reference for designing the SERS-involved therapeutic systems.

Bacteria Detection: From Powerful SERS to Its Advanced Compatible Techniques

The rapid, highly sensitive, and accurate detection of bacteria is the focus of various fields, especially food safety and public health. Surface-enhanced Raman spectroscopy (SERS), with the advantages of being fast, sensitive, and nondestructive, can be used to directly obtain molecular fingerprint information, as well as for the on-line qualitative analysis of multicomponent samples. It has therefore become an effective technique for bacterial detection. Within this progress report, advances in the detection of bacteria using SERS and other compatible techniques are discussed in order to summarize its development in recent years. First, the enhancement principle and mechanism of SERS technology are briefly overviewed. The second part is devoted to a label-free strategy for the detection of bacterial cells and bacterial metabolites. In this section, important considerations that must be made to improve bacterial SERS signals are discussed. Then, the label-based SERS strategy involves the design strategy of SERS tags, the immunomagnetic separation of SERS tags, and the capture of bacteria from solution and dye-labeled SERS primers. In the third part, several novel SERS compatible technologies and applications in clinical and food safety are introduced. In the final part, the results achieved are summarized and future perspectives are proposed.

Recent advances in surface-enhanced Raman scattering-based microdevices for point-of-care diagnosis of viruses and bacteria

This minireview reports the recent advances in surface-enhanced Raman scattering (SERS)-based assay devices for the diagnosis of infectious diseases. SERS-based detection methods have shown promise in overcoming the low sensitivity and multiplex detection problems inherent to fluorescence detection. Therefore, it is interesting to investigate the current status, challenges, and applications associated with SERS-based microdevices for the point-of-care (POC) diagnosis of infectious diseases. The majority of this review highlights three different types of microdevices, namely microfluidic channels, lateral flow assay strips, and three-dimensional nanostructured substrates. Furthermore, the integration of portable Raman spectrophotometry with microdevices provides an ideal platform for the diagnosis of various infectious diseases in the field. Integrated SERS-based assay systems also enable measurements in minimal sample volumes and at low analyte concentrations of viral or bacterial samples. A significant number of studies using the SERS-based assay system have been performed recently to realize POC diagnostics, especially under resource-limited conditions. This portable SERS sensor is expected to be a next-generation POC assay system that could overcome the limitations of current fluorescence-based assay systems. This minireview summarizes recent advances in the development of SERS-based microdevices for the diagnosis of infectious diseases. Lastly, challenges to overcome and future perspectives are discussed.

Monitoring Chemical Reactions with SERS-Active Ag-Loaded Mesoporous TiO2 Films

Monitoring chemical reactions that occur in small spaces or confined environments is challenging. Surface-enhanced Raman scattering (SERS) spectroscopy offers the unique possibility to monitor spectral changes with high sensitivity and time resolution. Herein, we report the application of composite mesoporous TiO₂ films loaded with Ag nanoparticles (NPs) to track in situ chemical processes in real time. In particular, the AgNPs@TiO₂ system was employed to monitor two chemical reactions: one occurring on the Ag NPs surface and another taking place in the surrounding solution. In the first case, we monitored the decarboxylation reaction of 4-mercaptobenzoic acid on Ag NPs, which allowed us to identify the conditions that favor it. In the second case, we studied the pH evolution in the nanocavities during a homogeneous alkalization process driven by chloride-assisted glycidol rupture (the Epoxide Route) and compared it with pH measurements by conventional techniques. We therefore demonstrated that the proposed nanodevice provides an excellent performance to monitor dynamic processes occurring either inside the material or in the solution in which it is immersed.

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.

Bacteria encapsulation and rapid antibiotic susceptibility test using a microfluidic microwell device integrating surface-enhanced Raman scattering

The antibiotic susceptibility test (AST) is a general laboratory procedure for bacterial identification and characterization and can be utilized to determine effective antimicrobials for individual patients. Due to the low bacterial concentration, conventional AST usually requires a prolonged bacterial culture time and a labor-intensive sample pretreatment process. Therefore, it cannot perform timely diagnosis or treatment, which results in a high mortality rate for seriously infected patients. To address this problem, we developed a microfluidic microwell device integrating surface-enhanced Raman scattering (SERS) technology, or the so called the Microwell-SERS system, to enable a rapid and high-throughput AST. Our results show that the Microwell-SERS system can successfully encapsulate bacteria in a miniaturized microwell with a greatly increased effective bacteria concentration, resulting in a shorter bacterial culture time. By attaching a microchannel onto the microwell, a smooth liquid and air exchange can purify the surrounding buffer and isolate bacteria in an individual microwell for independent SERS measurement. For proof-of-concept, we demonstrated a 2 h AST on susceptible and resistant E. coli and S. aureus with a concentration of 103 CFU mL-1 in the Microwell-SERS system, whereas the previous SERS-AST method required 108 CFU mL-1 bacterial suspension droplets dispensing on a SERS substrate. Based on the above features, we envision that the Microwell-SERS system could achieve highly sensitive, label-free, bacteria detection and rapid AST to enable timely and accurate bacterial infection disease diagnosis.

From single cells to complex tissues in applications of surface-enhanced Raman scattering

This tutorial review explores how three of the most common methods for introducing nanoparticles to single cells for surface-enhanced Raman scattering measurements can be adapted for experiments with complex tissues.

The laser-triggered dynamical plasmonic optical trapping of targets and advanced Raman detection sensitivity

Targets can be captured at hot spots during the laser-induced agglomeration of AgNPs via dynamical plasmonic optical trapping.