Applications of Fourier Transform-Infrared spectroscopy in microbial cell biology and environmental microbiology: advances, challenges, and future perspectives

Microbiological toxicity tests using standardized ISO/OECD methods-current state and outlook

Microbial toxicity tests play an important role in various scientific and technical fields including the risk assessment of chemical compounds in the environment. There is a large battery of normalized tests available that have been standardized by ISO (International Organization for Standardization) and OECD (Organization for Economic Co-operation and Development) and which are worldwide accepted and applied. The focus of this review is to provide information on microbial toxicity tests, which are used to elucidate effects in other laboratory tests such as biodegradation tests, and for the prediction of effects in natural and technical aqueous compartments in the environment. The various standardized tests as well as not normalized methods are described and their advantages and disadvantages are discussed. In addition, the sensitivity and usefulness of such tests including a short comparison with other ecotoxicological tests is presented. Moreover, the far-reaching influence of microbial toxicity tests on biodegradation tests is also demonstrated. A new concept of the physiological potential of an inoculum (PPI) consisting of microbial toxicity tests whose results are expressed as a chemical resistance potential (CRP) and the biodegradation adaptation potential (BAP) of an inoculum is described that may be helpful to characterize inocula used for biodegradation tests. KEY POINTS: • Microbial toxicity tests standardized by ISO and OECD have large differences in sensitivity and applicability. • Standardized microbial toxicity tests in combination with biodegradability tests open a new way to characterize inocula for biodegradation tests. • Standardized microbial toxicity tests together with ecotoxicity tests can form a very effective toolbox for the characterization of toxic effects of chemicals.

Fast Viral Diagnostics: FTIR-Based Identification, Strain-Typing, and Structural Characterization of SARS-CoV-2

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has triggered an ongoing global pandemic, necessitating rapid and accurate diagnostic tools to monitor emerging variants and preparedness for the next outbreak. This study introduces a multidisciplinary approach combining Fourier Transform Infrared (FTIR) microspectroscopy and Machine learning to comprehensively characterize and strain-type SARS-CoV-2 variants. FTIR analysis of pharyngeal swabs from different pandemic waves revealed distinct vibrational profiles, particularly in nucleic acid and protein vibrations. The spectral wavenumber range between 1150 and 1240 cm-1 was identified as the classification marker, distinguishing Healthy (noninfected) and infected samples. Machine learning algorithms, with neural networks exhibiting superior performance, successfully classified SARS-CoV-2 variants with a remarkable accuracy of 98.6%. Neural networks were also able to identify and differentiate a small cohort infected with influenza A variants, H1N1 and H3N2, from SARS-CoV-2-infected and Healthy samples. FTIR measurements further show distinct red shifts in vibrational energy and secondary structural alterations in the spike proteins of more transmissible forms of SARS-CoV-2 variants, providing experimental validation of the computational data. This integrated approach presents a promising avenue for rapid and reliable SARS-CoV-2 variant identification, enhancing our understanding of viral evolution and aiding in diagnostic advancements, particularly for an infectious disease with unknown etiology.

Zinc metal complexes synthesized by a green method as a new approach to alter the structural and optical characteristics of PVA: new field for polymer composite fabrication with controlled optical band gap

The current study employed a novel approach to design polymer composites with modified structural and declined optical band gaps. The results obtained in the present work for polymer composites can be considered an original method to make a new field for research based on green chemistry. Natural dyes extracted from green tea were mixed with hydrated zinc acetate (Zn(CH3COO)2·2H2O) to produce a metal complex. FTIR results comprehensively established the formation of the Zn-metal complex. The interaction among various components of PVA : Zn-metal complex composite was investigated using FTIR spectroscopy. The non-existence of anion bands of acetate in the Zn-metal complex spectrum confirms the formation of the Zn-metal complex. XRD analysis reveals that the Zn-metal complex improves the amorphous phase of the PVA-based composites. The absorption edge of the doped films shifted towards the lower photon energies. Optical dielectric properties were used to determine N/m*, ε ∞, τ, μ opt, ω p, and ρ opt; the W-D model was used to calculate E d, E o and n o parameters. The optical dielectric loss parameter was used to determine the optical band gap while the Tauc model was employed to identify various types of electron transitions. The optical energy band gap was 6.05 eV for clean PVA while it decreased to 1 eV for PVA inserted with the Zn-metal complex. The increase in Urbach energy from 0.26 eV to 0.45 eV is an evidence of the boost of amorphous phases in PVA : Zn-metal complex composites. The nonlinear refractive index and the first-order and second-order nonlinear optical susceptibilities were determined. The value of E o obtained from the W-D model closely matches the optical energy band gap obtained from the Tauc model, which indicates the precision of the analysis in the present study. The increase in SELF and VELF in the composite films establishes that new energy states assigned to the added Zn-metal complex amplify the probability of light-matter interaction.

A Comprehensive Methodology for Microbial Strain Typing Using Fourier-Transform Infrared Spectroscopy

Timely and accurate detection and characterization of microbial threats is crucial for effective infection and outbreak management. Additionally, in food production, rapid microbe identification is indispensable for maintaining quality control and hygiene standards. Current methods for typing microbial strains often rely on labor-intensive, time-consuming, and expensive DNA- and sera-serotyping techniques, limiting their applicability in rapid-response scenarios. In this context, the IR Biotyper®, utilizing Fourier-transform infrared (FTIR) spectroscopy, offers a novel approach, providing specific spectra for fast strain typing within 3 h. This methodology article serves as a comprehensive resource for researchers and technicians aiming to utilize FTIR spectroscopy for microbial strain typing. It encompasses detailed guidelines on sample preparation, data acquisition, and analysis techniques, ensuring the generation of reliable and reproducible results. We highlight the IR Biotyper®'s rapid and accurate discrimination capabilities, showcasing its potential for real-time pathogen monitoring and source-tracking to enhance public health and food safety. We propose its integration as an early screening method, followed by more detailed analysis with whole-genome sequencing, to optimize detection accuracy and response efficiency in microbial surveillance systems.

Oxidative stress responses in biofilms

Oxidizing agents are low-molecular-weight molecules that oxidize other substances by accepting electrons from them. They include reactive oxygen species (ROS), such as superoxide anions (O2-), hydrogen peroxide (H2O2), and hydroxyl radicals (HO-), and reactive chlorine species (RCS) including sodium hypochlorite (NaOCl) and its active ingredient hypochlorous acid (HOCl), and chloramines. Bacteria encounter oxidizing agents in many different environments and from diverse sources. Among them, they can be produced endogenously by aerobic respiration or exogenously by the use of disinfectants and cleaning agents, as well as by the mammalian immune system. Furthermore, human activities like industrial effluent pollution, agricultural runoff, and environmental activities like volcanic eruptions and photosynthesis are also sources of oxidants. Despite their antimicrobial effects, bacteria have developed many mechanisms to resist the damage caused by these toxic molecules. Previous research has demonstrated that growing as a biofilm particularly enhances bacterial survival against oxidizing agents. This review aims to summarize the current knowledge on the resistance mechanisms employed by bacterial biofilms against ROS and RCS, focussing on the most important mechanisms, including the formation of biofilms in response to oxidative stressors, the biofilm matrix as a protective barrier, the importance of detoxifying enzymes, and increased protection within multi-species biofilm communities. Understanding the complexity of bacterial responses against oxidative stress will provide valuable insights for potential therapeutic interventions and biofilm control strategies in diverse bacterial species.

Understanding the transition to viable but non-culturable state in Escherichia coli W3110: a comprehensive analysis of potential spectrochemical biomarkers

The viable but non-culturable (VBNC) state is considered a survival strategy employed by bacteria to endure stressful conditions, allowing them to stay alive. Bacteria in this state remain unnoticed in live cell counts as they cannot proliferate in standard culture media. VBNC cells pose a significant health risk because they retain their virulence and can revive when conditions normalize. Hence, it is crucial to develop fast, reliable, and cost-effective methods to detect bacteria in the VBNC state, particularly in the context of public health, food safety, and microbial control assessments. This research examined the biomolecular changes in Escherichia coli W3110 induced into the VBNC state in artificial seawater under three different stress conditions (temperature, metal, and antibiotic). Initially, confirmation of VBNC cells under various stresses was done using fluorescence microscopy and plate counts. Subsequently, lipid peroxidation was assessed through the TBARS assay, revealing a notable increase in peroxidation end-products in VBNC cells compared to controls. ATR-FTIR spectroscopy and chemomometrics were employed to analyze biomolecular changes, uncovering significant spectral differences in RNA, protein, and nucleic acid concentrations in VBNC cells compared to controls. Notably, RNA levels increased, while protein and nucleic acid amounts decreased. ROC analyses identified the 995 cm- 1 RNA band as a consistent marker across all studied stress conditions, suggesting its potential as a robust biomarker for detecting cells induced into the VBNC state under various stressors.

Stable Isotope Probing-nanoFTIR for Quantitation of Cellular Metabolism and Observation of Growth-Dependent Spectral Features

This study utilizes nanoscale Fourier transform infrared spectroscopy (nanoFTIR) to perform stable isotope probing (SIP) on individual bacteria cells cultured in the presence of 13C-labelled glucose. SIP-nanoFTIR simultaneously quantifies single-cell metabolism through infrared spectroscopy and acquires cellular morphological information via atomic force microscopy. The redshift of the amide I peak corresponds to the isotopic enrichment of newly synthesized proteins. These observations of single-cell translational activity are comparable to those of conventional methods, examining bulk cell numbers. Observing cells cultured under conditions of limited carbon, SIP- nanoFTIR is used to identify environmentally-induced changes in metabolic heterogeneity and cellular morphology. Individuals outcompeting their neighboring cells will likely play a disproportionately large role in shaping population dynamics during adverse conditions or environmental fluctuations. Additionally, SIP-nanoFTIR enables the spectroscopic differentiation of specific cellular growth phases. During cellular replication, subcellular isotope distribution becomes more homogenous, which is reflected in the spectroscopic features dependent on the extent of 13C-13C mode coupling or to specific isotopic symmetries within protein secondary structures. As SIP-nanoFTIR captures single-cell metabolism, environmentally-induced cellular processes, and subcellular isotope localization, this technique offers widespread applications across a variety of disciplines including microbial ecology, biophysics, biopharmaceuticals, medicinal science, and cancer research.

Application of Fourier Transform Infrared Spectroscopy to Discriminate Two Closely Related Bacterial Species: Bacillus anthracis and Bacillus cereus Sensu Stricto

Fourier transform infrared spectroscopy (FTIRS) is a diagnostic technique historically used in the microbiological field for the characterization of bacterial strains in relation to the specific composition of their lipid, protein, and polysaccharide components. For each bacterial strain, it is possible to obtain a unique absorption spectrum that represents the fingerprint obtained based on the components of the outer cell membrane. In this study, FTIRS was applied for the first time as an experimental diagnostic tool for the discrimination of two pathogenic species belonging to the Bacillus cereus group, Bacillus anthracis and Bacillus cereus sensu stricto; these are two closely related species that are not so easy to differentiate using classical microbiological methods, representing an innovative technology in the field of animal health.