Abstract
Vibrational spectroscopy is increasingly used for the rapid and non-destructive imaging of environmental and medical samples. Both Raman and Fourier-transform infrared (FT-IR) imaging have been applied to obtain detailed information on the chemical composition of biological materials, ranging from single microbial cells to tissues. Due to its compatibility with methods such as stable isotope labeling for the monitoring of cellular activities, vibrational spectroscopy also holds considerable power as a tool in microbial ecology. Chemical imaging of undisturbed biological systems (such as live cells in their native habitats) presents unique challenges due to the physical and chemical complexity of the samples, potential for spectral interference, and frequent need for real-time measurements. This Mini Review provides a critical synthesis of recent applications of Raman and FT-IR spectroscopy for characterizing complex biological samples, with a focus on developments in single-cell imaging. We also discuss how new spectroscopic methods could be used to overcome current limitations of single-cell analyses. Given the inherent complementarity of Raman and FT-IR spectroscopic methods, we discuss how combining these approaches could enable us to obtain new insights into biological activities either in situ or under conditions that simulate selected properties of the natural environment.
Highlights
Natural habitats are often physically and chemically complex, which has far-reaching consequences for the spatial distribution of microbial taxa and the processes they mediate (Resat et al, 2012; Vos et al, 2013; Pande et al, 2016; Ratzke and Gore, 2016)
Because controlled laboratory experiments rarely capture the heterogeneity present within natural environments, our knowledge of microbial activities is often based on indirect observation. To address this source of uncertainty, there is a need for methods that facilitate the in situ profiling of microorganisms and their activities in complex environments
While a limited number of studies have been published on Raman imaging of microbial strains or uncultured cells within their native environments, new instrumentation is likely to lead to an expansion of this field by enabling reduced spectral acquisition times without a loss of signal intensity (Opilik et al, 2013; Ando et al, 2016; Kano et al, 2016)
Summary
Natural habitats are often physically and chemically complex, which has far-reaching consequences for the spatial distribution of microbial taxa and the processes they mediate (Resat et al, 2012; Vos et al, 2013; Pande et al, 2016; Ratzke and Gore, 2016). Because controlled laboratory experiments rarely capture the heterogeneity present within natural environments, our knowledge of microbial activities is often based on indirect observation. To address this source of uncertainty, there is a need for methods that facilitate the in situ profiling of microorganisms and their activities in complex environments. Raman and infrared imaging have emerged as useful methods for the spatially resolved analysis of biological samples. Chemical Imaging of Complex Samples studies that have used these techniques to image single microbial cells within spatially and chemically complex environments These include pure cultures incubated in contact with physical substrata, multi-species assemblages within their native habitats, as well as other challenging sample types. State-of-the-art approaches for spectral imaging are critically evaluated in order to identify guidelines for future applications of single-cell analyses in microbial ecology
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