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

Abstract

Microorganisms play pivotal roles in shaping ecosystems and biogeochemical cycles. Their intricate interactions involve complex biochemical processes. Fourier Transform-Infrared (FT-IR) spectroscopy is a powerful tool for monitoring these interactions, revealing microorganism composition and responses to the environment. This review explores the diversity of applications of FT-IR spectroscopy within the field of microbiology, highlighting its specific utility in microbial cell biology and environmental microbiology. It emphasizes key applications such as microbial identification, process monitoring, cell wall analysis, biofilm examination, stress response assessment, and environmental interaction investigation, showcasing the crucial role of FT-IR in advancing our understanding of microbial systems. Furthermore, we address challenges including sample complexity, data interpretation nuances, and the need for integration with complementary techniques. Future prospects for FT-IR in environmental microbiology include a wide range of transformative applications and advancements. These include the development of comprehensive and standardized FT-IR libraries for precise microbial identification, the integration of advanced analytical techniques, the adoption of high-throughput and single-cell analysis, real-time environmental monitoring using portable FT-IR systems and the incorporation of FT-IR data into ecological modeling for predictive insights into microbial responses to environmental changes. These innovative avenues promise to significantly advance our understanding of microorganisms and their complex interactions within various ecosystems.

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

“…Infrared spectroscopy is based on the principle of measuring the absorption of infrared radiation by molecules [ 8 ]. Each molecule absorbs specific frequencies of infrared light that match the vibrational frequencies of their chemical bonds [ 23 ]. When infrared light interacts with a sample (bacterial or yeast cells), these wavelengths are absorbed by the sample’s molecular bonds, causing them to vibrate ( Figure 1 ).…”

“…However, other splicing methods focusing on regions corresponding to lipids, proteins, or proteins and carbohydrates can be applied ( Table 3 ). For a detailed description of other spectral windows, readers are referred to the review by Kassem et al [ 23 ]. It is also possible to create splicing methods that cover areas with high variance in the second derivative, either manually or through the software automatically (see Figure 4 ).…”

“…FTIR spectroscopy, like other strain typing methods, is not immune to limitations [ 23 , 28 ]. For instance, sample preparation requirements, including the need for specific sample forms and processing, if not done properly, can introduce artifacts [ 35 ].…”

“…Through FTIR spectroscopy, this system distinguishes strains by quantifying the absorption of infrared light by carbohydrates, lipids, nucleic acids, proteins, and lipopolysaccharides from microbial cells producing highly specific metabolic fingerprint-like signatures [ 8 , 21 ]. Several studies have shown that FTIR spectroscopy has high discriminatory power, enabling differentiation at the species or subspecies level [ 10 , 22 , 23 ]. It has been successfully employed for strain typing of pathogens such as Legionella pneumophila , Pseudomonas aeruginosa , Streptococcus pneumoniae , Bacillus cereus group, and Staphylococcus aureus [ 21 , 24 , 25 , 26 , 27 ].…”

“…It has been successfully employed for strain typing of pathogens such as Legionella pneumophila , Pseudomonas aeruginosa , Streptococcus pneumoniae , Bacillus cereus group, and Staphylococcus aureus [ 21 , 24 , 25 , 26 , 27 ]. A variety of FTIR-based methodologies have been utilized across microbial studies for tasks beyond microbial identification, such as process monitoring, cell wall analysis, biofilm examination, stress response assessment, and investigation of environmental interactions (reviewed by [ 23 , 28 ]). This versatility underscores the wide-ranging applications of FTIR spectroscopy in understanding microbial systems.…”