Raman microscopy and surface-enhanced Raman scattering (SERS) for in situ analysis of biofilms

Structural properties and microbial diversity of the biofilm colonizing plastic substrates in Terra Nova Bay (Antarctica)

Microbial colonization on plastic polymers has been extensively explored, however the temporal dynamics of biofilm community in Antarctic environments are almost unknown. As a contribute to fill this knowledge gap, the structural characteristics and microbial diversity of the biofilm associated with polyvinyl chloride (PVC) and polyethylene (PE) panels submerged at 5 m of depth and collected after 3, 9 and 12 months were investigated in four coastal sites of the Ross Sea. Additional panels placed at 5 and 20 m were retrieved after 12 months. Chemical characterization was performed by FTIR-ATR and Raman (through Surface-Enhanced Raman Scattering, SERS) spectroscopy. Bacterial community composition was quantified at a single cell level by Catalyzed Reporter Deposition Fluorescence In Situ Hybridization (CARD-FISH) and Confocal Laser Scanning Microscopy (CLSM); microbial diversity was assessed by 16S rRNA gene sequencing. This multidisciplinary approach has provided new insights into microbial community dynamics during biofouling process, shedding light on the biofilm diversity and temporal succession on plastic substrates in the Ross Sea. Significant differences between free-living and microbial biofilm communities were found, with a more consolidated and structured community composition on PVC compared to PE. Spectral features ascribable to tyrosine, polysaccharides, nucleic acids and lipids characterized the PVC-associated biofilms. Pseudomonadota (among Gamma-proteobacteria) and Alpha-proteobacteria dominated the microbial biofilm community. Interestingly, in Road Bay, close to the Italian "Mario Zucchelli" research station, the biofilm growth - already observed during summer season, after 3 months of submersion - continued afterwards leading to a massive microbial abundance at the end of winter (after 12 months). After 3 months, higher percentages of Gamma-proteobacteria in Road Bay than in the not-impacted site were found. These observations lead us to hypothesize that in this site microbial fouling developed during the first 3 months could serve as a starter pioneering community stimulating the successive growth during winter.

Improvement of a low-cost protocol for a simultaneous comparative evaluation of hydrolytic activity between sessile and planktonic cells: Candida albicans as a study model

Candida albicans is often implicated in nosocomial infections with fatal consequences. Its virulence is contributed to hydrolytic enzymes and biofilm formation. Previous research focused on studying these virulence factors individually. Therefore, this study aimed to investigate the impact of biofilm formation on the hydrolytic activity using an adapted low-cost method. Eleven strains of C. albicans were used. The biofilms were formed on pre-treated silicone discs using 24-well plates and then deposited on the appropriate agar to test each enzyme, while the planktonic cells were conventionally seeded. Biofilms were analysed using Raman spectroscopy, fluorescent and scanning electron microscopy. The adapted method provided an evaluation of hydrolytic enzymes activity in C. albicans biofilm and showed that sessile cells had a higher phospholipase and proteinase activities compared with planktonic cells. These findings were supported by spectroscopic and microscopic analyses, which provided valuable insights into the virulence mechanisms of C. albicans during biofilm formation.

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.

Contemporary strategies and approaches for characterizing composition and enhancing biofilm penetration targeting bacterial extracellular polymeric substances

Extracellular polymeric substances (EPS) constitutes crucial elements within bacterial biofilms, facilitating accelerated antimicrobial resistance and conferring defense against the host's immune cells. Developing precise and effective antibiofilm approaches and strategies, tailored to the specific characteristics of EPS composition, can offer valuable insights for the creation of novel antimicrobial drugs. This, in turn, holds the potential to mitigate the alarming issue of bacterial drug resistance. Current analysis of EPS compositions relies heavily on colorimetric approaches with a significant bias, which is likely due to the selection of a standard compound and the cross-interference of various EPS compounds. Considering the pivotal role of EPS in biofilm functionality, it is imperative for EPS research to delve deeper into the analysis of intricate compositions, moving beyond the current focus on polymeric materials. This necessitates a shift from heavy reliance on colorimetric analytic methods to more comprehensive and nuanced analytical approaches. In this study, we have provided a comprehensive summary of existing analytical methods utilized in the characterization of EPS compositions. Additionally, novel strategies aimed at targeting EPS to enhance biofilm penetration were explored, with a specific focus on highlighting the limitations associated with colorimetric methods. Furthermore, we have outlined the challenges faced in identifying additional components of EPS and propose a prospective research plan to address these challenges. This review has the potential to guide future researchers in the search for novel compounds capable of suppressing EPS, thereby inhibiting biofilm formation. This insight opens up a new avenue for exploration within this research domain.

Surface-enhanced Raman spectroscopy for characterization of supernatant samples of biofilm forming bacterial strains

Staphylococcus epidermidis is considered major cause of nosocomial infections. Its pathogenicity is mainly due to the ability to form biofilms on different surfaces, particularly indwelling medical devices. This bacterium consists of different strains consisting of non, medium and strong biofilm forming ones. Surface-enhanced Raman spectroscopy (SERS) is a powerful analytical technique that can be used to detect and analyze biochemical composition of the supernatant samples of different strains of bacteria including non, medium and strong biofilm forming bacterial strains. SERS is a powerful technique for the robust, reliable, rapid detection and discrimination of bacteria in the form of characteristic SERS spectral features which can be used for detection and classification. SERS is used to differentiate three classes of bacteria with respect to their biofilm forming ability. Silver nanoparticles (Ag NPs) are used as SERS substrate and synthesized with chemical reduction method. Principal component analysis (PCA) and partial least square discriminant analysis (PLS-DA) are used to discriminate SERS spectral data sets of non, medium and strong biofilm forming bacteria. PLS-DA analysis is a multivariate statistical technique that can be used to analyze data from bacterial sets.

In Situ Spatiotemporal SERS Measurements and Multivariate Analysis of Virally Infected Bacterial Biofilms Using Nanolaminated Plasmonic Crystals

In situ spatiotemporal biochemical characterization of the activity of living multicellular biofilms under external stimuli remains a significant challenge. Surface-enhanced Raman spectroscopy (SERS), combining the molecular fingerprint specificity of vibrational spectroscopy with the hotspot sensitivity of plasmonic nanostructures, has emerged as a promising noninvasive bioanalysis technique for living systems. However, most SERS devices do not allow reliable long-term spatiotemporal SERS measurements of multicellular systems because of challenges in producing spatially uniform and mechanically stable SERS hotspot arrays to interface with large cellular networks. Furthermore, very few studies have been conducted for multivariable analysis of spatiotemporal SERS datasets to extract spatially and temporally correlated biological information from multicellular systems. Here, we demonstrate in situ label-free spatiotemporal SERS measurements and multivariate analysis of Pseudomonas syringae biofilms during development and upon infection by bacteriophage virus Phi6 by employing nanolaminate plasmonic crystal SERS devices to interface mechanically stable, uniform, and spatially dense hotspot arrays with the P. syringae biofilms. We exploited unsupervised multivariate machine learning methods, including principal component analysis (PCA) and hierarchical cluster analysis (HCA), to resolve the spatiotemporal evolution and Phi6 dose-dependent changes of major Raman peaks originating from biochemical components in P. syringae biofilms, including cellular components, extracellular polymeric substances (EPS), metabolite molecules, and cell lysate-enriched extracellular media. We then employed supervised multivariate analysis using linear discriminant analysis (LDA) for the multiclass classification of Phi6 dose-dependent biofilm responses, demonstrating the potential for viral infection diagnosis. We envision extending the in situ spatiotemporal SERS method to monitor dynamic, heterogeneous interactions between viruses and bacterial networks for applications such as phage-based anti-biofilm therapy development and continuous pathogenic virus detection.

Impact of Fe2+ and Shear Stress on the Development and Mesoscopic Structure of Biofilms-A Bacillus subtilis Case Study

Bivalent cations are known to affect the structural and mechanical properties of biofilms. In order to reveal the impact of Fe²⁺ ions within the cultivation medium on biofilm development, structure and stability, Bacillus subtilis biofilms were cultivated in mini-fluidic flow cells. Two different Fe²⁺ inflow concentrations (0.25 and 2.5 mg/L, respectively) and wall shear stress levels (0.05 and 0.27 Pa, respectively) were tested. Mesoscopic biofilm structure was determined daily in situ and non-invasively by means of optical coherence tomography. A set of ten structural parameters was used to quantify biofilm structure, its development and change. The study focused on characterizing biofilm structure and development at the mesoscale (mm-range). Therefore, biofilm replicates (n = 10) were cultivated and analyzed. Three hypotheses were defined in order to estimate the effect of Fe²⁺ inflow concentration and/or wall shear stress on biofilm development and structure, respectively. It was not the intention to investigate and describe the underlying mechanisms of iron incorporation as this would require a different set of tools applied at microscopic levels as well as the use of, i.e., omic approaches. Fe²⁺ addition influenced biofilm development (e.g., biofilm accumulation) and structure markedly. Experiments revealed the accumulation of FeO(OH) within the biofilm matrix and a positive correlation of Fe²⁺ inflow concentration and biofilm accumulation. In more detail, independent of the wall shear stress applied during cultivation, biofilms grew approximately four times thicker at 2.5 mg Fe²⁺/L (44.8 µmol/L; high inflow concentration) compared to the low Fe²⁺ inflow concentration of 0.25 mg Fe²⁺/L (4.48 µmol/L). This finding was statistically verified (Scheirer-Ray-Hare test, ANOVA) and hints at a higher stability of Bacillus subtilis biofilms (e.g., elevated cohesive and adhesive strength) when grown at elevated Fe²⁺ inflow concentrations.

Advances in Detection of Antibiotic Pollutants in Aqueous Media Using Molecular Imprinting Technique-A Review

Antibiotics constitute one of the emerging categories of persistent organic pollutants, characterised by their expansion of resistant pathogens. Antibiotic pollutants create a major public health challenge, with already identifiable detrimental effects on human and animal health. A fundamental aspect of controlling and preventing the spread of pollutants is the continuous screening and monitoring of environmental samples. Molecular imprinting is a state-of-the-art technique for designing robust biomimetic receptors called molecularly imprinted polymers (MIPs), which mimic natural biomolecules in target-selective recognition. When integrated with an appropriate sensor transducer, MIP demonstrates a potential for the needed environmental monitoring, thus justifying the observed rise in interest in this field of research. This review examines scientific interventions within the last decade on the determination of antibiotic water pollutants using MIP receptors interfaced with label-free sensing platforms, with an expanded focus on optical, piezoelectric, and electrochemical systems. Following these, the review evaluates the analytical performance of outstanding MIP-based sensors for environmentally significant antibiotics, while highlighting the importance of computational chemistry in functional monomer selection and the strategies for signal amplification and performance improvement. Lastly, the review points out the future trends in antibiotic MIP research, as it transits from a proof of concept to the much demanded commercially available entity.

Silver Mesoporous Silica Nanoparticles: Fabrication to Combination Therapies for Cancer and Infection

The integration of silver nanoparticles (Ag NPs) with mesoporous silica nanoparticles (MSNs) protects the former from aggregation and promotes the controlled release of silver ions, resulting in therapeutic significance on cancer and infection. The unique size, shape, pore structure and silver distribution of silver mesoporous silica nanoparticles (Ag-MSNs) embellish them with the potential to perform combined imaging and therapeutic actions via modulating optical and drug release properties. Here, we comprehensively review the recent progress in the fabrication and application of Ag-MSNs for combination therapies for cancer and infection. We first elaborate on the fabrication of star-shaped structure, core-shell structure, and Janus structure Ag-MSNs. We then highlight Ag-MSNs as a multifunctional nanoplatform to surface-enhanced Raman scattering-based detection, non-photo-based cancer theranostics and photo-based cancer theranostics. In addition, we detail Ag-MSNs for combined antibacterial therapy via drug delivery and phototherapy. Overall, we summarize the challenges and future perspectives of Ag-MSNs that make them promising for diagnosis and therapy of cancer and infection.

Optical nanosensors for biofilm detection in the food industry: principles, applications and challenges

Biofilms are the universal lifestyle of bacteria enclosed in extracellular polymeric substances (EPS) on the contact surfaces of food processing facilities. The EPS-encapsulated foodborne bacterial pathogens are the main food contaminant sources, posing a serious threat to human health. The microcrystalline, sophisticated and dynamic biofilms necessitate the development of conventional microscopic imaging and spectral technology. Nanosensors, which can transfer the biochemical information into optical signals, have recently emerged for biofilm optical detection with high sensitivity and high spatial resolution at nanoscale scopes. Therefore, the aim of this review is to clarify the main detection scope in biofilms and the detection principles of optical nanosensors arousing Raman enhancement, fluoresce conversion and color change. The difficulties and challenges of biofilm characterization including the secretion and variation of main biochemical components are first discussed, the details about the principles and application examples of bioassays targeting foodborne pathogens based on optical nanosensors are then summarized. Finally, the challenges and future trends in developing optical nanosensors are also highlighted. The current review indicates that optical nanosensors have taken the challenges of detecting biofilm in complex food samples, including the characterization of biofilm formation mechanism, identification of microbial metabolic activities, diagnosis of potential food pathogens and sanitation monitoring of food processing equipment. Numerous in-depth explorations and various trials have proven that the bioassays based on multifunctional optical nanosensors are promising to ensure and promote food safety and quality. However, there still remains a daunting challenge to structure reproducible, biocompatible and applicable nano-sensors for biofilm characterization, identification, and imaging.

Heteroresistant Bacteria Detected by an Extended Raman-Based Antibiotic Susceptibility Test

Worldwide, multiresistant bacterial strains are emerging at unprecedented rates. This development seriously threatens the ability of humanity to treat even common infections, resulting in disability and death. Furthermore, this development endangers all medical achievements including cancer therapy or organ transplantations. Therefore, the World Health Organization has endorsed antimicrobial resistance as a great threat to humanity. To still allow effective treatment of patients, rapid, automated, and reliable antibiotic susceptibility testing (AST) of bacterial pathogens is essential. Thereby, speed and sensitivity of the AST results are crucial for improving patient care. Here, Raman spectroscopy as a nondestructive technique providing chemical-specific information is employed to monitor the deuterium uptake of metabolically active bacteria during antibiotic treatment, enabling fast and reliable AST. For this purpose, a bulk sample-preparation method was developed, allowing a high-throughput analysis of a significant number of cells. A protocol was developed for Gram-positive (Enterococcus faecalis) and Gram-negative (Escherichia coli) reference strains and was tested on 51 clinical isolates with well-characterized resistance phenotypes against ampicillin, ciprofloxacin, meropenem, and vancomycin. Borderline resistant and heteroresistant phenotypes were observed and further investigated. This is of critical importance as the sensitive detection of low-frequency heteroresistance in bacterial populations is a huge challenge. Such isolates seem susceptible but are resistant to treatment in vivo. Automatable analysis detects strong phenotypes within 3 h. On the basis of experimental and modeled data, heteroresistance is estimated to be detectable down to frequencies of 10^-6 and investigated on clinical isolates as a proof-of-concept study, but requiring longer incubation time.

The FT-IR and Raman Spectroscopies as Tools for Biofilm Characterization Created by Cariogenic Streptococci

Fourier transform infrared (FT-IR) and Raman spectroscopy and mapping were applied to the analysis of biofilms produced by bacteria of the genus Streptococcus. Bacterial biofilm, also called dental plaque, is the main cause of periodontal disease and tooth decay. It consists of a complex microbial community embedded in an extracellular matrix composed of highly hydrated extracellular polymeric substances and is a combination of salivary and bacterial proteins, lipids, polysaccharides, nucleic acids, and inorganic ions. This study confirms the value of Raman and FT-IR spectroscopies in biology, medicine, and pharmacy as effective tools for bacterial product characterization.

Gold and silver nanoparticles used for SERS detection of S. aureus and E. coli

Surface enhanced Raman scattering (SERS) is emerging as a robust analytical method used in sensing applications in chemical as well as biological systems. SERS has been reported to be used in fast detection of micro-organisms up to the specificity of strain identification. However, use of SERS is tricky because of difficulties involved in selection of SERS active substrate so as to give uniform, sensitive as well as reproducible results. We have synthesized silver and gold nanoparticles using chemical, electrochemical and microwave-assisted methods followed by their characterization. Uses of these nanoparticles in association with micro-organisms such as S. aureus and E. coli have been analyzed using SERS to generate signature spectra. This demonstrates use of so synthesized gold and silver nanoparticles as SERS active substrates for rapid detection of micro-organisms which pave way to find applications in disease diagnostics.

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.

Quantitative imaging and spectroscopic technologies for microbiology

Light microscopy has enabled the observation of the structure and organisation of biofilms. Typically, the contrast in an image obtained from light microscopy is given by the time-averaged intensity that is effective in visualising the overall structure. Technological advancements in light microscopy have led to the creation of techniques that not only provide a static intensity image of the biofilm, but also enable one to quantify various dynamic physicochemical properties of biomolecules in microbial biofilms. Such light microscopy-based techniques can be grouped into two main classes, those that are based on luminescence and those that are based on scattering. Here, we review the fundamentals and applications of luminescence and scattering-based techniques, specifically, fluorescence lifetime imaging, Förster resonance energy transfer, fluorescence correlation spectroscopy, fluorescence recovery after photobleaching, single-particle tracking, transient state imaging, and Brillouin and Raman microscopy. These techniques provide information about the abundance, interactions and mobility of various molecules in the biofilms and also properties of the local microenvironment at optical resolution. Further, one could use any of these techniques to probe the real-time changes in these physical parameters upon the addition of external agents or at different stages during the growth of biofilms.

Biofilm systems as tools in biotechnological production

The literature provides more and more examples of research projects that develop novel production processes based on microorganisms organized in the form of biofilms. Biofilms are aggregates of microorganisms that are attached to interfaces. These viscoelastic aggregates of cells are held together and are embedded in a matrix consisting of multiple carbohydrate polymers as well as proteins. Biofilms are characterized by a very high cell density and by a natural retentostat behavior. Both factors can contribute to high productivities and a facilitated separation of the desired end-product from the catalytic biomass. Within the biofilm matrix, stable gradients of substrates and products form, which can lead to a differentiation and adaptation of the microorganisms' physiology to the specific process conditions. Moreover, growth in a biofilm state is often accompanied by a higher resistance and resilience towards toxic or growth inhibiting substances and factors. In this short review, we summarize how biofilms can be studied and what most promising niches for their application can be. Moreover, we highlight future research directions that will accelerate the advent of productive biofilms in biology-based production processes.

High Correlation Between Structure Development and Chemical Variation During Biofilm Formation by Vibrio parahaemolyticus

The complex three-dimensional structure of biofilms is supported by extracellular polymeric substances (EPSs) and additional insight on chemical variations in EPS and biofilm structure development will inform strategies for control of biofilms. Vibrio parahaemolyticus VPS36 biofilm development was studied using confocal laser scanning microscopy (CLSM) and Raman spectroscopy (RM). The structural parameters of the biofilm (biovolume, mean thickness, and porosity) were characterized by CLSM and the results showed that VPS36 biofilm formed dense structures after 48 h incubation. There were concurrent variations in carbohydrates and nucleic acids contents in the EPS as evidenced by RM. The Raman intensities of the chemical component in EPS, measured using Pearson's correlation coefficient, were positively correlated with biovolume and mean thickness, and negatively correlated with porosity. The Raman intensity for carbohydrates correlated closely with mean thickness (p-value < 0.01) and the Raman intensity for nucleic acid correlated closely with porosity (p-value < 0.01). Additional evidence for these correlations were confirmed using scanning electron microscopic (SEM) and crystal violet staining.

Surface-Enhanced Raman Scattering Spectroscopy for Label-Free Analysis of P. aeruginosa Quorum Sensing

Bacterial quorum sensing systems regulate the production of an ample variety of bioactive extracellular compounds that are involved in interspecies microbial interactions and in the interplay between the microbes and their hosts. The development of new approaches for enabling chemical detection of such cellular activities is important in order to gain new insight into their function and biological significance. In recent years, surface-enhanced Raman scattering (SERS) spectroscopy has emerged as an ultrasensitive analytical tool employing rationally designed plasmonic nanostructured substrates. This review highlights recent advances of SERS spectroscopy for label-free detection and imaging of quorum sensing-regulated processes in the human opportunistic pathogen Pseudomonas aeruginosa. We also briefly describe the challenges and limitations of the technique and conclude with a summary of future prospects for the field.

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.

It is all about location: how to pinpoint microorganisms and their functions in multispecies biofilms

Multispecies biofilms represent the dominant mode of life for the vast majority of microorganisms. Bacterial spatial localization in such biostructures governs ecological interactions between different populations and triggers the overall community functions. Here, we discuss the pros and cons of fluorescence-based techniques used to decipher bacterial species patterns in biofilms at single cell level, including fluorescence in situ hybridization and the use of genetically modified bacteria that express fluorescent proteins, reporting the significant improvements of those techniques. The development of tools for spatial and temporal study of multispecies biofilms will allow live imaging and spatial localization of cells in naturally occurring biofilms coupled with metabolic information, increasing insight of microbial community and the relation between its structure and functions.

Understanding and Discrimination of Biofilms of Clinically Relevant Microorganisms Using Surface-Enhanced Raman Scattering

Biofilm formation is a defense mechanism for microorganisms to survive under both natural and stress conditions. Clinically relevant microorganisms threaten patient health through biofilm formation on medical devices and implants. It is very important to identify biofilm formation in order to suppress their pathogenic activities in early stages. With the aim for better understanding biofilm formation and possibility of detection, in this study, biofilm formation of clinically important microorganisms, Pseudomonas aeruginosa, Staphylococcus epidermidis, and Candida albicans are monitored with surface-enhanced Raman scattering (SERS). The SERS spectra were collected by mapping a dried droplet area where a volume of colloidal silver nanoparticle (AgNP) suspension is placed on microorganism culture plate. The spectral changes on the SERS spectra with increasing incubation time of the model microorganisms from 4 to 120 h are monitored. The unique spectra originating from the biofilms of three pathogenic microorganisms and the spectral changes as a result of time-dependent concentration fluctuations of biomolecular species in their biofilms including carbohydrates, lipids, proteins, and genetic materials allow not only identification but also discrimination of biofilms using principal component analysis.

Elucidation of impact of heavy metal pollution on soil bacterial growth and extracellular polymeric substances flexibility

Metal bioaccessibility is an alarming issue in croplands of mining sites due to overloading of toxic metals. Hence, the present study is aimed to determine the overloading of toxic metal in croplands across the Tawag village, Hutti, Raichur, India. Correspondingly, to identify the soil bacterial growth, physiological oxidative stress enzyme activity and surface macromolecular functional group evolution were analysed in and around the toxic metal contaminated sites through FT-IR and FT-Raman spectrometry. The evaluated results attribute that the study area is heavily polluted with the toxic metals such as arsenic, cadmium, chromium, lead and zinc. However, biochemical and 16S rRNA gene sequence homology tree confirmed that the arsenic and cadmium-resistant isolate belongs to Bacillus sp. MDPMK-02 and retrieved unique Gene Bank ID KT596811 (accession number) at National Centre for Biotechnology information (NCBI), India. Additionally, sodium arsenite-amended culture media possessing reduced biomass and enhanced the activity of oxidative stress defence enzymes such as superoxide dismutase (SOD) and catalase (CAT) than cadmium chloride-amended medium and control. Subsequently, the infrared (IR) and Raman spectral analytical assessment distinguish that arsenic-treated Gram-positive isolate membrane fetched high percentage of hydration, elevation of surface polysaccharides, proteins and polyhydroxybutyric acid (PHBA) molecular specific stretch intensity compared to cadmium exposures. From these results, the study concluded that the mining wastes significantly pollute the surrounding croplands, and also Bacillus sp. MDPMK-02 possesses good chemosensing for cross-protection and bio-adaptation of toxic metal ions. Hence, these isolates can be compiled and implemented in environmental hazardous management techniques such as bioremediation, bioleaching and biodegradation.

RhizoFlowCell system reveals early effects of micropollutants on aquatic plant rhizosphere

In aquatic systems, one of the non-destructive ways to quantify toxicity of contaminants to plants is to monitor changes in root exudation patterns. In aquatic conditions, monitoring and quantifying such changes are currently challenging because of dilution of root exudates in water phase and lack of suitable instrumentation to measure them. Exposure to pollutants would not only change the plant exudation, but also affect the microbial communities that surround the root zone, thereby changing the metabolic profiles of the rhizosphere. This study aims at developing a device, the RhizoFlowCell, which can quantify metabolic response of plants, as well as changes in the microbial communities, to give an estimate of the stress to which the rhizosphere is exposed. The usefulness of RhizoFlowCell is demonstrated using naphthalene as a test pollutant. Results show that RhizoFlowCell system is useful in quantifying the dynamic metabolic response of aquatic rhizosphere to determine ecosystem health.

Influence of various chloride ion concentrations on silver nanoparticle transformations and effectiveness in surface enhanced Raman scattering for different excitation wavelengths

This study reports the effect of six various concentrations of chlorides on the surface enhanced Raman scattering activity of silver nanoparticles.

Combination of synchrotron radiation-based Fourier transforms infrared microspectroscopy and confocal laser scanning microscopy to understand spatial heterogeneity in aquatic multispecies biofilms

Understanding the spatial heterogeneity within environmental biofilms can provide an insight into compartmentalization of different functions in biofilm communities. We used a non-destructive and label-free method by combining Synchrotron Radiation-based Fourier Transform Infrared Microspectroscopy (SR-FTIR) with Confocal Laser Scanning Microscopy (CLSM) to distinguish the spatial chemical changes within multispecies biofilms grown from natural storm waters in flow cells. Among the different surfaces tested for biofilm growth and optimal imaging, mylar membranes were most suited and it enabled successful spatial infrared imaging of natural biofilms for obtaining reliable and interpretable FTIR spectra. Time series analysis of biofilm growth showed that influx of water during biofilm growth, results in significant changes in biofilm formation. Early biofilms showed active nutrient acquisition and desiccation tolerance mechanisms corresponding with accumulation of secreted proteins. Statistical approach used for the evaluation of chemical spectra allowed for clustering and classification of various regions of the biofilm. Microheterogeneity was observed in the polymeric components of the biofilm matrix, including cellulose, glycocalyx and dextran-like molecules. Fructan and glycan-rich regions were distinguishable and glycocalyx was abundant in the strongly adhering peripheral regions of biofilms. Inner core showed coexistence of oxygen dimers and ferrihydrite that will likely support growth of Fe (II)-oxidising bacteria. The combined SR-FTIR microspectroscopy and CSLM approach for complex natural biofilms described here will be useful both in understanding heterogeneity of matrix components and in correlating functions of juxtaposed microbial species in complex natural biofilms with physicochemical microenvironment to which they are exposed.

Spatial organization of Pseudomonas aeruginosa biofilms probed by combined matrix-assisted laser desorption ionization mass spectrometry and confocal Raman microscopy

The chemical composition of bacterial biofilms is explored and visualized with the combination of two label-free molecular imaging techniques.

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

A ratiometric luminescence intensity imaging approach is presented, which enables spatial O2 measurements in biofilm reactors with transparent planar O2 optodes. Optodes consist of an O2 sensitive luminescent dye immobilized in a 1-10 μm thick polymeric layer on a transparent carrier, e.g. a glass window. The method is based on sequential imaging of the O2 dependent luminescence intensity, which are subsequently normalized with luminescent intensity images recorded under anoxic conditions. We present 2-dimensional O2 distribution images at the base of a tap water biofilm measured with the new ratiometric method and compare the results with O2 distribution images obtained in the same biofilm reactor with luminescence lifetime imaging. Using conventional digital cameras, such simple normalized luminescence intensity imaging can yield images of 2-dimensional O2 distributions with a high signal-to-noise ratio and spatial resolution comparable or even surpassing those obtained with expensive and complex luminescence lifetime imaging systems. The method can be applied to biofilm growth incubators allowing intermittent experimental shifts to anoxic conditions or in systems, in which the O2 concentration is depleted during incubation.

Label-free in situ SERS imaging of biofilms

Surface-enhanced Raman scattering (SERS) is a promising technique for the chemical characterization of biological systems. It yields highly informative spectra, can be applied directly in aqueous environment, and has high sensitivity in comparison with normal Raman spectroscopy. Moreover, SERS imaging can provide chemical information with spatial resolution in the micrometer range (chemical imaging). In this paper, we report for the first time on the application of SERS for in situ, label-free imaging of biofilms and demonstrate the suitability of this technique for the characterization of the complex biomatrix. Biofilms, being communities of microorganisms embedded in a matrix of extracellular polymeric substances (EPS), represent the predominant mode of microbial life. Knowledge of the chemical composition and the structure of the biofilm matrix is important in different fields, e.g., medicine, biology, and industrial processes. We used colloidal silver nanoparticles for the in situ SERS analysis. Good SERS measurement reproducibility, along with a significant enhancement of Raman signals by SERS (>10(4)) and highly informative SERS signature, enables rapid SERS imaging (1 s for a single spectrum) of the biofilm matrix. Altogether, this work illustrates the potential of SERS for biofilm analysis, including the detection of different constituents and the determination of their distribution in a biofilm even at low biomass concentration.