Transcriptional heterogeneity of catabolic genes on the plasmid pCAR1 causes host-specific carbazole degradation.

To elucidate why plasmid-borne catabolic ability differs among host bacteria, we assessed the expression dynamics of the Pant promoter on the carbazole-degradative conjugative plasmid pCAR1 in Pseudomonas putida KT2440(pCAR1) (hereafter, KTPC) and Pseudomonas resinovorans CA10. The Pant promoter regulates the transcription of both the car and ant operons, which are responsible for converting carbazole into anthranilate and anthranilate into catechol, respectively. In the presence of anthranilate, transcription of the Pant promoter is induced by the AraC/XylS family regulator AntR, encoded on pCAR1. A reporter cassette containing the Pant promoter followed by gfp was inserted into the chromosomes of KTPC and CA10. After adding anthranilate, GFP expression in the population of CA10 showed an unimodal distribution, whereas a small population with low GFP fluorescence intensity appeared for KTPC. CA10 has a gene, antRCA, that encodes an iso-functional homolog of AntR on its chromosome. When antRCA was disrupted, a small population with low GFP fluorescence intensity appeared. In contrast, overexpression of pCAR1-encoded AntR in KTPC resulted in unimodal expression under the Pant promoter. These results suggest that the expression of pCAR1-encoded AntR is insufficient to ameliorate the stochastic expression of the Pant promoter. Raman spectra of single cells collected using deuterium-labeled carbazole showed that the C-D Raman signal exhibited greater variability for KTPC than CA10. These results indicate that heterogeneity at the transcriptional level of the Pant promoter due to insufficient AntR availability causes fluctuations in the pCAR1-borne carbazole-degrading capacity of host bacterial cells.IMPORTANCEHorizontally acquired genes increase the competitiveness of host bacteria under selective conditions, although unregulated expression of foreign genes may impose fitness costs. The "appropriate" host for a plasmid is empirically known to maximize the expression of plasmid-borne traits. In the case of pCAR1-harboring Pseudomonas strains, P. resinovorans CA10 exhibits strong carbazole-degrading capacity, whereas P. putida KT2440 harboring pCAR1 exhibits low degradation capacity. Our results suggest that a chromosomally encoded transcription factor affects transcriptional and metabolic fluctuations in host cells, resulting in different carbazole-degrading capacities as a population. This study may provide a clue for determining appropriate hosts for a plasmid and for regulating the expression of plasmid-borne traits, such as the degradation of xenobiotics and antibiotic resistance.

Observation of the Pockels Effect in Ionic Liquids and Insights into the Length Scale of Potential-Induced Ordering.

Ionic liquids (ILs) under electric fields play essential roles in the electrochemical utilization of ILs. Recently, long-range organization of ILs in the vicinity of charged (and even neutral) surfaces has been revealed, but experimental evidence for such an ordering is still limited and its spatial length scale remains controversial. Here, we use confocal Raman microspectroscopy to investigate the effect of an applied electric potential on the IL 1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide and its analogues in a space-resolved manner. Much to our surprise, the observed Raman difference spectra of the ILs obtained with and without an applied potential exhibit uniform intensity changes independent of vibrational modes of cations and anions, a finding in sharp contrast with the electric field effects on molecular liquids that we have previously observed. We interpret this unexpected finding in terms of the Pockels effect that occurs as a result of a potential-induced ordering of the IL near an IL-electrode interface. The refractive index changes due to the applied potential are estimated using the experimental Raman intensity changes. The results allow us to deduce that the length scale of the ordering in the ILs is tens to hundreds of nanometers, extending more than would be expected for the electrical double layer but not as far as a micrometer scale.

Interactions of water confined in a metal-organic framework as studied by a combined approach of Raman, FTIR, and IR electroabsorption spectroscopies and multivariate curve resolution analysis.

Water in nanoconfinement shows distinct properties that are markedly different from those of bulk water. These unique properties stem not only from the water-water interaction but also from the interactions between water and the surrounding confining environment. Here we used a combined approach of vibrational spectroscopies (Raman, FTIR, and IR electroabsorption) and a multivariate curve resolution technique to study the interactions of water in a heterogeneous confining environment within a prototype of pillared layer-type metal-organic frameworks (MOFs), CPL-1 ([Cu2(pzdc)2(pyz)]n, where pzdc = 2,3-pyrazinedicarboxylate, pyz = pyrazine). The OH stretching Raman spectrum of hydrated CPL-1 microcrystals revealed that the adsorbed water molecules resemble the subpopulation of bulk water whose hydrogen bond is weak. Multivariate curve resolution analysis of FTIR spectra monitoring water desorption from CPL-1 allowed for accurate assignments of the framework's carboxylate vibrational modes associated with water-filled and empty nanopores of the MOF, and for quantitative determination of the number fraction of these pores. Furthermore, building on the assignments so made, IR electroabsorption measurements showed that the hydrogen-bonding interaction with water adsorbed in CPL-1 has little impact on the response to electric fields of the framework vibrational modes. The present findings altogether provide a solid basis of elucidating water confined in CPL-1 and demonstrate the potential of the combined vibrational spectroscopic method for interrogating the interactions within MOFs.

Inhomogeneous Molecular Distributions and Cytochrome Types and Redox States in Fungal Cells Revealed by Raman Hyperspectral Imaging Using Multivariate Curve Resolution-Alternating Least Squares.

Hyphae of filamentous fungi consist of compartments that are distinct both spatially and functionally, thereby forming a unique multicellular system. Much work has been done mainly using fluorescence imaging to reveal what biomolecules are present in those different hyphal sections and what physiological roles they play. Nevertheless, a holistic understanding of hyphal functions including the polarized growth of hyphae is still lacking because of the difficulty in simultaneous acquisition of spatial and chemical information on various molecular components in living hyphae. Here, we used a multivariate curve resolution-alternating least-squares (MCR-ALS) analysis of Raman hyperspectral imaging data to study in vivo the spatial distributions and chemical properties of major cellular components in the tip, basal, and branching regions of the model fungus Aspergillus nidulans. The MCR-ALS Raman imaging method visualized, without any labeling, the characteristic distributions of cytochromes as well as other components including polysaccharides, noncytochrome proteins, nucleic acids, lipids, and ergosterol in the hyphal regions studied. Furthermore, the intrinsic Raman spectra derived for the first time from the MCR-ALS analysis enabled us to gain otherwise unobtainable chemical insights into those visualized components. We show variations in the relative abundance of cytochromes b and c and in their redox states (reduced vs oxidized form) among the three different representative compartments of A. nidulans hyphae, which could potentially be associated with specific physiological activities and functions of hyphae. The present results demonstrate that our MCR-ALS Raman imaging can serve as a useful tool complementary to the conventional approaches, for elucidating the diverse roles of filamentous fungi at the molecular level.

Complementing Crystallography with Ultralow-Frequency Raman Spectroscopy: Structural Insights into Nitrile-Functionalized Ionic Liquids.

Functionalized ionic liquids are a subclass of ionic liquids that are tailored for a specific application. Structural characterization in both solid and liquid phases is central to understanding their physical properties. Here, we used ultralow-frequency Raman spectroscopy, which can measure Raman spectra down to approximately 5 cm(-1) , to study the structures and physical properties of 1-(4-cyanobenzyl)-3-methylimidazolium salts with five different anions. A comparison of the observed low-frequency Raman spectral patterns enabled us to predict the crystal symmetry of one of the synthesized salts for which single-crystal X-ray diffraction data were unobtainable. Real-time tracking of the low-frequency Raman spectral changes during melting revealed peak shifts indicative of different degrees of microscopic heterogeneity in the ionic liquids. The results show that our method provides a facile means that is complementary to X-ray crystallography, for obtaining structural information of ionic liquids.

Significance of weak interactions in imidazolium picrate ionic liquids: spectroscopic and theoretical studies for molecular level understanding.

The effects of interionic hydrogen bonding and π-π stacking interactions on the physical properties of a new series of picrate anion based ionic liquids (ILs) have been investigated experimentally and theoretically. The existence of aromatic (C2-HO) and aliphatic (C7-HO-N22 and C6-HO-N20) hydrogen bonding and π-π stacking interactions in these ILs has been observed using various spectroscopic techniques. The aromatic and aliphatic C-HO hydrogen bonding interactions are found to have a crucial role in binding the imidazolium cation and picrate anion together. However, the π-π stacking interactions between two successive layers are found to play a decisive role in tight packing in ILs leading to differences in physical properties. The drastic difference in the melting points of the methyl and propyl derivatives (mmimPic and pmimPic respectively) have been found to be primarily due to the difference in the strength and varieties of π-π stacking interactions. While in mmimPic, several different types of π-π stacking interactions between the aromatic rings (such as picrate-picrate, picrate-imidazole and imidazolium-imidazolium cation rings) are observed, only one type of π-π stacking interaction (picrate-picrate rings) is found to exist in the pmimPic IL. NMR spectroscopic studies reveal that the interaction of these ILs with solvent molecules is different and depends on the dielectric constant of the solvent. While an ion solvation model explains the solvation in high dielectric solvents, an ion-pair solvation model is found to be more appropriate for low dielectric constant solvents. The enhanced stability of these investigated picrate ILs compared with that of inorganic picrate salts under high doses of γ radiation clearly indicates the importance of weak interionic interactions in ILs, and also opens up the possibility of the application of picrate ILs as prospective diluents in nuclear separation for advanced fuel cycling process.

Exploring metabolic pathways in vivo by a combined approach of mixed stable isotope-labeled Raman microspectroscopy and multivariate curve resolution analysis.

Understanding cellular metabolism is a major challenge in current systems biology and has triggered extensive metabolomics research, which in most cases involves destructive analysis. However, the information obtainable only in a nondestructive manner will be required for accurately mapping the global structure of the organism's metabolic network at a given instant. Here we report that metabolic pathways can be explored in vivo by mixed stable isotope-labeled Raman microspectroscopy in conjunction with multivariate curve resolution analysis. As a model system, we studied ergosterol biosynthesis in single living fission yeast cells grown in mixtures of normal and (13)C-labeled glucose as the sole carbon source. The multivariate spectral data analysis of space-resolved Raman spectra revealed the intrinsic spectra and relative abundances of all isotopomers of ergosterol whose carbon atoms in the 5,7-diene moiety of the sterol skeleton are either partly or fully substituted with (13)C. Our approach is applicable to other metabolites and will earn a place in the toolbox of metabolomic analysis.

Mechanism of back electron transfer in an intermolecular photoinduced electron transfer reaction: solvent as a charge mediator.

Back electron transfer (BET) is one of the important processes that govern the decay of generated ion pairs in intermolecular photoinduced electron transfer reactions. Unfortunately, a detailed mechanism of BET reactions remains largely unknown in spite of their importance for the development of molecular photovoltaic structures. Here, we examine the BET reaction of pyrene (Py) and 1,4-dicyanobenzene (DCB) in acetonitrile (ACN) by using time-resolved near- and mid-IR spectroscopy. The Py dimer radical cation (Py2(·+)) and DCB radical anion (DCB(·-)) generated after photoexcitation of Py show asynchronous decay kinetics. To account for this observation, we propose a reaction mechanism that involves electron transfer from DCB(·-) to the solvent and charge recombination between the resulting ACN dimer anion and Py2(·+). The unique role of ACN as a charge mediator revealed herein could have implications for strategies that retard charge recombination in dye-sensitized solar cells.

Correlation of carotenoid accumulation with aggregation and biofilm development in Rhodococcus sp. SD-74.

Aggregation of bacterial populations substantially influences their characteristic properties and functions compared with the planktonic counterpart. It is also involved in the initial stages of biofilm development. Many studies have revealed important roles of bacterial aggregation in microbial production and biodegradation. Nevertheless, mechanistic understanding of bacterial aggregation in vivo and at the molecular level is far from complete. Here, we present a noninvasive, label-free Raman microspectroscopic approach to investigate the aggregation and biofilm development of the biotechnologically important Rhodococcus sp. SD-74. We found that the concentration of intracellular carotenoids increases more than 3-fold within 1 week as the biofilm develops. Raman imaging experiments confirmed that the carotenoid accumulation occurs throughout the Rhodococcus sp. SD-74 biofilm. The correlation between the carotenoid Raman intensities and biofilm development found in the present study provides a new means for quantitative, molecular-level assessment of the level of biofilm development, which is not possible with dye staining assay or electron microscopy. Moreover, our results suggest that microbial production of carotenoids in pigmented bacteria such as Rhodococcus sp. SD-74 may potentially be controlled via bacterial aggregation and biofilm formation.

In vivo probing of the temperature responses of intracellular biomolecules in yeast cells by label-free Raman microspectroscopy.

Environmental temperature is an essential physical quantity that substantially influences cell physiology by changing the equilibria and kinetics of biochemical reactions occurring in cells. Although it has been extensively used as a readily controllable parameter in genetic and biochemical research, much remains to be explored about the temperature responses of intracellular biomolecules in vivo and at the molecular level. Here we report in vivo probing, achieved with label-free Raman microspectroscopy, of the temperature responses of major intracellular components such as lipids and proteins in living fission yeast cells. The characteristic Raman band at 1602 cm(-1), which has been attributed mainly to ergosterol, showed a significant decrease (≈47 %) in intensity at elevated temperatures above 35 °C. In contrast to this high temperature sensitivity of the ergosterol Raman band, the phospholipid and protein Raman bands did not vary much with increasing culture temperature in the 26-38 °C range. This finding agrees with a previous biochemical study that showed that the initial stages of ergosterol biosynthesis in yeast are hindered by temperature elevation. Moreover, our result demonstrates that Raman microspectroscopy holds promise for elucidation of temperature-dependent cellular activities in living cells, with a high molecular specificity that the commonly used fluorescence microscopy cannot offer.

Simultaneous Imaging and Characterization of Polyunsaturated Fatty Acids, Carotenoids, and Microcrystalline Guanine in Single Aurantiochytrium limacinum Cells with Linear and Nonlinear Raman Microspectroscopy.

Thraustochytrids are heterotrophic marine protists known for their high production capacity of various compounds with health benefits, such as polyunsaturated fatty acids and carotenoids. Although much effort has been focused on developing optimal cultivation methods for efficient microbial production, these high-value compounds and their interrelationships are not well understood at the single-cell level. Here we used spontaneous (linear) Raman and multiplex coherent anti-Stokes Raman scattering (CARS) microspectroscopy to visualize and characterize lipids (e.g., docosahexaenoic acid) and carotenoids (e.g., astaxanthin) accumulated in single living Aurantiochytrium limacinum cells. Spontaneous Raman imaging with the help of multivariate curve resolution-alternating least-squares enabled us to make unambiguous assignments of the molecular components we detected and derive their intracellular distributions separately. Near-IR excited CARS imaging yielded the Raman images at least an order of magnitude faster than spontaneous Raman imaging, with suppressed contributions of carotenoids. As the culture time increased from 2 to 5 days, the lipid amount increased by a factor of ∼7, whereas the carotenoid amount did not change significantly. Furthermore, we observed a highly localized component in A. limacinum cells. This component was found to be mixed crystals of guanine and other purine derivatives. The present study demonstrates the potential of the linear-nonlinear Raman hybrid approach that allows for accurate molecular identification and fast imaging in a label-free manner to link information derived from single cells with strategies for mass culture of useful thraustochytrids.

Disentangling dynamic changes of multiple cellular components during the yeast cell cycle by in vivo multivariate Raman imaging.

Cellular processes are intrinsically complex and dynamic, in which a myriad of cellular components including nucleic acids, proteins, membranes, and organelles are involved and undergo spatiotemporal changes. Label-free Raman imaging has proven powerful for studying such dynamic behaviors in vivo and at the molecular level. To construct Raman images, univariate data analysis has been commonly employed, but it cannot be free from uncertainties due to severely overlapped spectral information. Here, we demonstrate multivariate curve resolution analysis for time-lapse Raman imaging of a single dividing yeast cell. A four-dimensional (spectral variable, spatial positions in the two-dimensional image plane, and time sequence) Raman data "hypercube" is unfolded to a two-way array and then analyzed globally using multivariate curve resolution. The multivariate Raman imaging thus accomplished successfully disentangles dynamic changes of both concentrations and distributions of major cellular components (lipids, proteins, and polysaccharides) during the cell cycle of the yeast cell. The results show a drastic decrease in the amount of lipids by ~50% after cell division and uncover a protein-associated component that has not been detected with previous univariate approaches.

Is our way of thinking about excited states correct? Time-resolved dispersive IR study on p-nitroaniline.

Low-lying excited electronic states of an important class of molecules known as push-pull chromophores are central to understanding their potential nonlinear optical properties. Here we report that a combination of high-sensitivity nanosecond time-resolved dispersive IR spectroscopy and DFT calculations on p-nitroaniline (PNA), a prototypical push-pull molecule, reveals that PNA in the lowest excited triplet state has a partial quinoid structure. In this structure, the quinoid configuration is restricted to a part of the phenyl ring adjacent to the NO(2) group. The partial quinoid structure of PNA cannot be explained by a commonly used hybrid of a neutral form and a zwitterionic charge-transfer form. Our findings not only cast doubt on the general applicability of the classical way of looking at excited states, based exclusively on characteristic resonance structures, but also provide deeper insights into excited-state structure of highly polarizable molecular systems.

Anharmonic coupling of the CH-stretch and CH-bend vibrations of chloroform as studied by near-infrared electroabsorption spectroscopy.

Combination bands that involve CH- or OH-stretch vibrations appear in the near-infrared (NIR) region (4000-10 000 cm(-1)). Because they arise from anharmonic coupling between the component fundamentals, detailed analysis of the frequency and intensity of NIR combination bands allows one to elucidate the mechanisms behind the vibrational coupling in the condensed phase in terms of mechanical and electrical anharmonicities. Nevertheless, little has been studied, in particular experimentally, on the origin of the combination band intensity. Here, we show that NIR electroabsorption (EA) spectroscopy, which directly probes the effects of an externally applied electric field on a combination band, can shed new light on anharmonic vibrational coupling through determination of the direction of the transition moment for the combination band. We studied the combination band of the CH-stretch (ν(1)) and CH-bend (ν(4)) modes of liquid chloroform. The electric-field induced absorbance change of the ν(1) + ν(4) combination band caused by reorientation of the chloroform molecule was measured at various χ angles, where χ is the angle between the direction of the applied electric field and the polarization of the incident IR light. We were able to detect an absorbance change as small as 5 × 10(-8) for the combination band. Using the NIR EA spectra of the combination band together with those of the CH-stretch and bend fundamentals, the angle between the transition moment for the combination band and the permanent dipole moment was determined experimentally for the first time to be (79 ± 14)°. The present investigation indicates that the contribution of the CH-stretch mode to the mechanical anharmonicity is minor and that the CH-bend mode plays a dominant role in the mechanical part of the vibrational coupling between the two fundamentals. Furthermore, density functional theory calculations show that both the mechanical anharmonicity of the CH-bend mode and the electrical anharmonicity may contribute equally to the anharmonic coupling.

Raman Micro-spectroscopy and Imaging of Filamentous Fungi.

Filamentous fungi grow by the elongation of tubular cells called hyphae and form mycelia through repeated hyphal tip growth and branching. Since hyphal growth is closely related to the ability to secrete large amounts of enzymes or invade host cells, a more detailed understanding and the control of its growth are important in fungal biotechnology, ecology, and pathogenesis. Previous studies using fluorescence imaging revealed many of the molecular mechanisms involved in hyphal growth. Raman microspectroscopy and imaging methods are now attracting increasing attention as powerful alternatives due to their high chemical specificity and label-free, non-destructive properties. Spatially resolved information on the relative abundance, structure, and chemical state of multiple intracellular components may be simultaneously obtained. Although Raman studies on filamentous fungi are still limited, this review introduces recent findings from Raman studies on filamentous fungi and discusses their potential use in the future.

Resonance Raman analysis of intracellular vitamin B12 analogs in methanogenic archaea.

Methanogenic archaea (methanogens) are microorganisms that can synthesize methane. They are found in diverse environments ranging from paddy fields to animal digestive tracts to deep-sea hydrothermal vents. Investigating their distribution and physiological activity is crucial for the detailed analysis of the dynamics of greenhouse gas generation and the search for the environmental limits of life. In methanogens, cobamide cofactors (vitamin B12 analogs) play a key role in methane synthesis and carbon fixation, thus serving as a marker compound that metabolically characterizes them. Here, we report on resonance Raman detection of cobamides in methanogenic cells without destroying cells and provide structural insights into those cobamides. We succeeded in detecting cobamides in four representative methanogens Methanosarcina mazei, Methanosarcina barkeri, Methanopyrus kandleri, and Methanocaldococcus jannaschii. The former two are mesophilic, cytochrome-containing methanogens, whereas the latter two are hyperthermophilic, non-cytochrome-containing methanogens. The 532 nm-excited Raman spectra of single or multiple cells of the four species all showed resonance Raman bands of cobamides arising mainly from the corrin ring, with the most intense one at ∼1500 cm-1. We envision that resonance Raman microspectroscopy could be useful for in situ, nondestructive identification of methanogenic cells that produce high levels of cobamides.

Nondestructive microbial discrimination using single-cell Raman spectra and random forest machine learning algorithm.

Raman microspectroscopy is a powerful tool for obtaining biomolecular information from single microbial cells in a nondestructive manner. Here, we detail steps to discriminate prokaryotic species using single-cell Raman spectra acquisitions followed by data preprocessing and random forest model tuning. In addition, we describe the steps required to evaluate the model. This protocol requires minimal preprocessing of Raman spectral data, making it accessible to non-spectroscopists, yet allows intuitive visualization of feature importance. For complete details on the use and execution of this protocol, please refer to Kanno et al. (2021).

Infrared electroabsorption spectroscopy of N,N-dimethyl-p-nitroaniline in acetonitrile/C2Cl4: solvation of the solute and self-association of acetonitrile.

Solvated structures of N,N-dimethyl-p-nitroaniline (DMPNA), an analog of p-nitroaniline (PNA), and self-associated structures of acetonitrile (ACN) in mixed solvents of ACN and C(2)Cl(4) were studied using infrared (IR) electroabsorption and FTIR spectroscopies. IR electroabsorption spectroscopy measures changes in IR absorption intensity upon application of external electric field modulation, which are a sensitive probe for permanent dipole moments. In ACN/CCl(4), PNA has been shown to occur as two distinct solvated forms, namely, 1:1 and 1:2 forms, which have one and two ACN molecule(s), respectively, associated with PNA. The IR electroabsorption and FTIR measurements on DMPNA show that, unlike PNA, DMPNA occurs as a monomer in ACN/C(2)Cl(4) rather than as specific solvated structures analogous to the 1:1 and 1:2 forms because of the substitution effect. Not only does the N,N-dimethyl substitution in DMPNA hamper solvation of ACN at the N(CH(3))(2) group, but it also indirectly blocks strong interactions with ACN at the NO(2) group. Furthermore, by using the ΔA signal of DMPNA as an internal intensity standard, it was found that the dipole moment of ACN in the DMPNA/ACN/C(2)Cl(4) system is about 1.5 times larger than that of the ACN monomer in dilute CCl(4) solution. This large value of the dipole moment in the solution studied here is attributable to the formation of a head-to-tail linear dimer of ACN, whereas the antiparallel dimer is energetically more favorable in the gas phase.

Deuterium-labeled Raman tracking of glucose accumulation and protein metabolic dynamics in Aspergillus nidulans hyphal tips.

Filamentous fungi grow exclusively at their tips, where many growth-related fungal processes, such as enzyme secretion and invasion into host cells, take place. Hyphal tips are also a site of active metabolism. Understanding metabolic dynamics within the tip region is therefore important for biotechnology and medicine as well as for microbiology and ecology. However, methods that can track metabolic dynamics with sufficient spatial resolution and in a nondestructive manner are highly limited. Here we present time-lapse Raman imaging using a deuterium (D) tracer to study spatiotemporally varying metabolic activity within the hyphal tip of Aspergillus nidulans. By analyzing the carbon-deuterium (C-D) stretching Raman band with spectral deconvolution, we visualize glucose accumulation along the inner edge of the hyphal tip and synthesis of new proteins from the taken-up D-labeled glucose specifically at the central part of the apical region. Our results show that deuterium-labeled Raman imaging offers a broadly applicable platform for the study of metabolic dynamics in filamentous fungi and other relevant microorganisms in vivo.

Machine learning-assisted single-cell Raman fingerprinting for in situ and nondestructive classification of prokaryotes.

Accessing enormous uncultivated microorganisms (microbial dark matter) in various Earth environments requires accurate, nondestructive classification, and molecular understanding of the microorganisms in in situ and at the single-cell level. Here we demonstrate a combined approach of random forest (RF) machine learning and single-cell Raman microspectroscopy for accurate classification of phylogenetically diverse prokaryotes (three bacterial and three archaeal species from different phyla). Our RF classifier achieved a 98.8 ± 1.9% classification accuracy among the six species in pure populations and 98.4% for three species in an artificially mixed population. Feature importance scores against each wavenumber reveal that the presence of carotenoids and structure of membrane lipids play key roles in distinguishing the prokaryotic species. We also find unique Raman markers for an ammonia-oxidizing archaeon. Our approach with moderate data pretreatment and intuitive visualization of feature importance is easy to use for non-spectroscopists, and thus offers microbiologists a new single-cell tool for shedding light on microbial dark matter.