Raman Microscopic Analysis of Single Microbial Cells

Magnaporthe grisea cutinase2 mediates appressorium differentiation and host penetration and is required for full virulence

The rice blast fungus Magnaporthe grisea infects its host by forming a specialized infection structure, the appressorium, on the plant leaf. The enormous turgor pressure generated within the appressorium drives the emerging penetration peg forcefully through the plant cuticle. Hitherto, the involvement of cutinase(s) in this process has remained unproven. We identified a specific M. grisea cutinase, CUT2, whose expression is dramatically upregulated during appressorium maturation and penetration. The cut2 mutant has reduced extracellular cutin-degrading and Ser esterase activity, when grown on cutin as the sole carbon source, compared with the wild-type strain. The cut2 mutant strain is severely less pathogenic than the wild type or complemented cut2/CUT2 strain on rice (Oryza sativa) and barley (Hordeum vulgare). It displays reduced conidiation and anomalous germling morphology, forming multiple elongated germ tubes and aberrant appressoria on inductive surfaces. We show that Cut2 mediates the formation of the penetration peg but does not play a role in spore or appressorium adhesion, or in appressorial turgor generation. Morphological and pathogenicity defects in the cut2 mutant are fully restored with exogenous application of synthetic cutin monomers, cAMP, 3-isobutyl-1-methylxanthine, and diacylglycerol (DAG). We propose that Cut2 is an upstream activator of cAMP/protein kinase A and DAG/protein kinase C signaling pathways that direct appressorium formation and infectious growth in M. grisea. Cut2 is therefore required for surface sensing leading to correct germling differentiation, penetration, and full virulence in this model fungus.

Microbial communities in anaerobic digestion processes for waste and wastewater treatment: a microbiological update

Anaerobic digestion technology is the biological treatment of organic waste and wastewater without input of external electron acceptors (oxygen), offering the potential to reduce treatment cost and to produce energy as 'biogas' (methane) from organic waste. The technology has become enormously popular in the past two decades, and knowledge of microbiological aspects of the technology has also accumulated significantly. Major advances have been made in elucidating the diversity of yet-to-be cultured microbes in anaerobic digestion processes, and the cultivation of uncultured organisms is of great interest with regard to gaining insights into the function of these organisms. In addition, recent advances have been made in the development of microbial fuel cells as an alternative, direct energy-yielding treatment system.

Who eats what, where and when? Isotope-labelling experiments are coming of age

Isotope-labelling experiments have changed the way microbial ecologists investigate the ecophysiology of microbial populations and cells in the environment. Insight into the 'uncultivated majority' accompanies methodology that involves the incorporation of stable isotopes or radioisotopes into sub-populations of environmental samples. Subsequent analysis of labelled biomarkers of sub-populations with stable-isotope probing (DNA-SIP, RNA-SIP, phospholipid-derived fatty acid-SIP) or individual cells with a combination of fluorescence in situ hybridization and microautoradiography reveals linked phylogenetic and functional information about the organisms that assimilated these compounds. Here, we review some of the most recent literature, with an emphasis on methodological improvements to the sensitivity and utility of these methods. We also highlight related isotope techniques that are in continued development and hold promise to transform the way we link phylogeny and function in complex microbial communities.

Methodological considerations for the use of stable isotope probing in microbial ecology

Stable isotope probing (SIP) is a method used for labeling uncultivated microorganisms in environmental samples or directly in field studies using substrate enriched with stable isotope (e.g., (13)C). After consumption of the substrate, the cells of microorganisms that consumed the substrate become enriched in the isotope. Labeled biomarkers, such as phospholipid-derived fatty acid (PLFA), ribosomal RNA, and DNA can be analyzed with a range of molecular and analytical techniques, and used to identify and characterize the organisms that incorporated the substrate. The advantages and disadvantages of PLFA-SIP, RNA-SIP, and DNA-SIP are presented. Using examples from our laboratory and from the literature, we discuss important methodological considerations for a successful SIP experiment.

The environmental plasmid pQBR103 alters the single-cell Raman spectral profile of Pseudomonas fluorescens SBW25

Although plasmids are ubiquitous amongst phytosphere pseudomonads, the advantage and costs of plasmids for the bacterial host remain unclear. The application of single-cell Raman spectral analysis to plasmid-bacterial systems under different environmental conditions offers a new means of determining the impact of plasmids on host cell physiology, metabolic status, and response to stress.

Pseudomonas fluorescens SBW25 biofilm and planktonic cells have differentiable Raman spectral profiles

Biofilms, and other bacterial aggregations, are of significance in both environmental microbiology and in plant and human pathogenesis. Comparative single-cell Raman spectral analysis can differentiate between planktonic bacteria and those recovered from biofilms and appears to offer a new means by which to investigate bacterial cell physiology, metabolic status, and stress under different environmental conditions.

Single-cell Raman spectral profiles of Pseudomonas fluorescens SBW25 reflects in vitro and in planta metabolic history

Single-cell Raman microspectroscopy has the potential to report on the whole-cell chemical composition of bacteria, reflecting metabolic status as well as growth history. This potential has been demonstrated through the discriminant functional analysis of Raman spectral profiles (RSP) obtained from the soil and plant-associated bacterium Pseudomonas fluorescens SBW25, grown in vitro using defined media, and in planta using 3-month-old sugar beets (Beta vulgaris var. Roberta). SBW25 in vitro RSP data showed significant variation between those cells grown on different amino acids, sugars, TCA cycle intermediates, rich King's B, and culture media derived from the sugar beet phytosphere. Raman analysis was also able to follow the transition of SBW25 starved of carbon over a period of days, and SBW25 in planta RSP data also showed variation with significant differences between bacteria recovered from soil and the rhizosphere. SBW25 whole-cell chemical composition, and therefore growth and metabolic history, could be interpreted by coanalyzing in vitro and in planta RSP data. SBW25 recovered from the phytosphere was found to be more similar to SBW25 grown in vitro on Fru or Asp, rather than on Glc or Arg, and quite dissimilar to that resulting from carbon starvation. This suggests that SBW25 growth in the phytosphere is generally neither carbon-catabolite-repressed nor carbon-limited. These findings demonstrate that the analysis of single-cell RSP can differentiate between isogenic populations of bacteria with different metabolic histories or after recovery from different parts of their natural environment. In addition, Raman analysis is also capable of providing biologically relevant biochemical inferences, which might then be tested to uncover the mechanistic basis (biochemical-metabolic-genetic) differentiating bacteria growing in complex environments and exposed to different conditions.

Synthesis and characterization of CN-modified protein analogues as potential vibrational contrast agents

A recombinant VH single-domain antibody recognizing staphylococcal protein A was functionalized on reactive lysine residues with N-hydroxysuccimidyl-activated 4-cyanobenzoate. Surface plasmon resonance analysis of antibody-antigen binding revealed that modified and unmodified antibodies bound protein A with similar affinities. Raman imaging of the modified antibodies indicated that the benzonitrile group provides vibrational contrast enhancement in a region of the electromagnetic spectrum that is transparent to cellular materials. Thus, the modified single-domain antibody may be amenable to detecting protein A from samples of the human pathogen Staphylococcus aureus using vibronic detection schemes such as Raman and coherent anti-Stokes Raman scattering. The generality of this labeling strategy should make it applicable to modifying an array of proteins with varied structure and function.

Chemotaxonomical identification of spores of macrofungi: possibilities of Raman spectroscopy

Confocal Raman spectroscopy is a non-destructive analytical method which is useful to obtain detailed information about the molecular composition of biological samples. Its high spatial resolution was used to collect spectra of single basidiospores of macrofungi of the genera Collybia, Gymnopus, Laccaria, Lactarius, Mycena and Russula. These spectra can be divided into three major taxon-related groups, with general compositional differences, such as the relative amount of lipids compared to proteins. In this study, collapsing of thin-walled spores during storage was often observed, a phenomenon which has been given little attention in the literature. The Raman spectra are treated with different chemometric preprocessing techniques, including Savitsky-Golay, standard normal variate (SNV) preprocessing and extended multiplicative scatter correction (EMSC). By using linear discriminant analysis, approximately 90% of the spectra can be assigned to the correct genus, but identification on the species level was not possible.

Towards a Detailed Understanding of Bacterial Metabolism—Spectroscopic Characterization ofStaphylococcus Epidermidis

Bacteria are a major cause of infection. To fight disease and growing resistance, research interest is focused on understanding bacterial metabolism. For a detailed evaluation of the involved mechanisms, a precise knowledge of the molecular composition of the bacteria is required. In this article, various vibrational spectroscopic techniques are applied to comprehensively characterize, on a molecular level, bacteria of the strain Staphylococcus epidermidis, an opportunistic pathogen which has evolved to become a major cause of nosocomial infections. IR absorption spectroscopy reflects the overall chemical composition of the cells, with major focus on the protein vibrations. Smaller sample volumes-down to a single cell-are sufficient to probe the overall chemical composition by means of micro-Raman spectroscopy. The nucleic-acid and aromatic amino-acid moieties are almost exclusively explored by UV resonance Raman spectroscopy. In combination with statistical evaluation methods [hierarchical cluster analysis (HCA), principal component analysis (PCA), linear discriminant analysis (LDA)], the protein and nucleic-acid components that change during the different bacterial growth phases can be identified from the in vivo vibrational spectra. Furthermore, tip-enhanced Raman spectroscopy (TERS) provides insight into the surface structures and follows the dynamics of the polysaccharide and peptide components on the bacterial cells with a spatial resolution below the diffraction limit. This might open new ways for the elucidation of host-bacteria and drug-bacteria interactions.

Rapid characterization of microbial biodegradation pathways by FT-IR spectroscopy

Fourier transform-infrared (FT-IR) spectroscopy has become an important tool for rapid analysis of complex biological samples. The infrared absorbance spectrum could be regarded as a "fingerprint" which is characteristic of biochemical substances. In this study, Pseudomonas putida NCIMB 9869 was grown with either 3,5-xylenol or m-cresol as the sole carbon source, each inducing different metabolic pathways for m-cresol biotransformation. FT-IR spectroscopy was capable of differentiating both induced cultures of P. putida NCIMB 9869 as well as the resulting biotransformation product mixtures. FT-IR spectral analysis indicated that carboxylic acids were key chemicals responsible for distinguishing the products of the two catabolic pathways. Gas chromatography-mass spectrometry (GC-MS) was performed to validate the FT-IR analysis, indicating that two carboxylic acids, 3-hydroxybenzoic acid and 2,5-dihydroxybenzoic acid, were present as m-cresol biotransformation products from 3,5-xylenol-grown cells, but were absent in m-cresol-grown cells. The ability to use FT-IR to rapidly distinguish between biotransformation product mixtures as well as differentially induced bacterial strains suggests this approach might be a valuable tool for screening large biotransformation assays for novel products and metabolic mutants.

In situ characterisation of a microorganism surface by Raman microspectroscopy: the shell of Ascaris eggs

Intestinal nematodes are very common human parasites and a single species, Ascaris lumbricoïdes, is estimated to infect a quarter of the world's population. A sticky external layer covers their eggs. This work shows that Raman vibrational confocal spectroscopy is able to give information on the biochemical composition of the shell of Ascaris eggs. The biochemical localised characterisation of Ascaris eggs was performed directly on the eggs in their aqueous environment. The studied parasites came from two origins: dissections of adult females and extractions from biosolid sludges. The presence of mucopolysaccharides, proteins and chitin in the shell was demonstrated. The presence of ascaroside compounds was shown particularly via the narrow and intense bands from the organised long CH2 chains. To the best of our knowledge, this is the first time that the latter have been observed in Raman vibrational spectra of microorganisms. Hydration of the shell was different depending on the intensity of the colour of the sludge eggs. Knowledge of the biochemical structural properties of egg surfaces would be useful to understand the egg adhesion phenomena on vegetables contaminated by reused wastewater.

Consideration of Future Requirements for Raman Microbiology as an Examplar for the Ab Initio Development of Informatics Frameworks for Emergent OMICS Technologies

Raman spectroscopy of single bacteria provides an OMIC-like view of the chemical status of individual cells, reporting on metabolism, cell stress and growth, and is likely to become a significant tool in environmental and medical microbiology. We advocate the early development of integrated data models and informatics frameworks, in parallel with the development of Raman hardware and experimental protocols, in order to maximize the benefits of this emerging OMIC technology to the research community.

Metabolic fingerprinting in disease diagnosis: biomedical applications of infrared and Raman spectroscopy

The ability to diagnose the early onset of disease, rapidly, non-invasively and unequivocally has multiple benefits. These include the early intervention of therapeutic strategies leading to a reduction in morbidity and mortality, and the releasing of economic resources within overburdened health care systems. Some of the routine clinical tests currently in use are known to be unsuitable or unreliable. In addition, these often rely on single disease markers which are inappropriate when multiple factors are involved. Many diseases are a result of metabolic disorders, therefore it is logical to measure metabolism directly. One of the strategies employed by the emergent science of metabolomics is metabolic fingerprinting; which involves rapid, high-throughput global analysis to discriminate between samples of different biological status or origin. This review focuses on a selective number of recent studies where metabolic fingerprinting has been forwarded as a potential tool for disease diagnosis using infrared and Raman spectroscopies.

Unlocking the ‘microbial black box’ using RNA-based stable isotope probing technologies

Microbial ecologists have long sought to associate the transformation of compounds in the environment with the microbial clades responsible. The development of stable isotope probing (SIP) has made this possible in many ecological and biotechnological contexts. RNA-based SIP technologies represent a significant leap forward for culture-independent 'functional phylogeny' analyses, where specific consumption of a given compound carrying a (13)C signature can be associated with the small subunit ribosomal RNA molecules of the microbes that consume it. Recent advances have led to the unequivocal identification of microorganisms responsible for contaminant degradation in engineered systems, and to applications enhancing our understanding of carbon flow in terrestrial ecosystems.

Use of field-based stable isotope probing to identify adapted populations and track carbon flow through a phenol-degrading soil microbial community

The goal of this field study was to provide insight into three distinct populations of microorganisms involved in in situ metabolism of phenol. Our approach measured 13CO2 respired from [13C]phenol and stable isotope probing (SIP) of soil DNA at an agricultural field site. Traditionally, SIP-based investigations have been subject to the uncertainties posed by carbon cross-feeding. By altering our field-based, substrate-dosing methodologies, experiments were designed to look beyond primary degraders to detect trophically related populations in the food chain. Using gas chromatography-mass spectrometry (GC/MS), it was shown that (13)C-labeled biomass, derived from primary phenol degraders in soil, was a suitable growth substrate for other members of the soil microbial community. Next, three dosing regimes were designed to examine active members of the microbial community involved in phenol metabolism in situ: (i) 1 dose of [13C]phenol, (ii) 11 daily doses of unlabeled phenol followed by 1 dose of [13C]phenol, and (iii) 12 daily doses of [13C]phenol. GC/MS analysis demonstrated that prior exposure to phenol boosted 13CO2 evolution by a factor of 10. Furthermore, imaging of 13C-treated soil using secondary ion mass spectrometry (SIMS) verified that individual bacteria incorporated 13C into their biomass. PCR amplification and 16S rRNA gene sequencing of 13C-labeled soil DNA from the 3 dosing regimes revealed three distinct clone libraries: (i) unenriched, primary phenol degraders were most diverse, consisting of alpha-, beta-, and gamma-proteobacteria and high-G+C-content gram-positive bacteria, (ii) enriched primary phenol degraders were dominated by members of the genera Kocuria and Staphylococcus, and (iii) trophically related (carbon cross-feeders) were dominated by members of the genus Pseudomonas. These data show that SIP has the potential to document population shifts caused by substrate preexposure and to follow the flow of carbon through terrestrial microbial food chains.

Spectroscopic analysis of Kaposi's sarcoma-associated herpesvirus infected cells by Raman tweezers

Kaposi's sarcoma-associated herpesvirus (KSHV), also referred to as human herpesvirus-8 (HHV-8), is a tumor causing virus. KSHV is the cause of several disease conditions known as Kaposi's sarcoma, multicentric Castleman disease, and primary effusion lymphoma. Cell culture supernatants from KSHV infected hematopoietic cells induced angiogenic tubule formation to a significantly greater extent than uninfected hematopoietic cells. Raman spectrum profiles were generated to differentiate the uninfected from KSHV infected cells. In general, profiles from all the hematopoietic cells shared similar peaks; however, the relative abundance of specific components varied significantly between the cells. Subsequent use of the multivariate analysis of the Raman spectra revealed significant differences between the uninfected and the KSHV infected cells. Taken together, this study reports the use of Raman tweezers to distinguish and analyze the biological relevance of KSHV infected cell signaling.

Bioaugmentation for bioremediation: the challenge of strain selection

Despite its long-term use in bioremediation, bioaugmentation of contaminated sites with microbial cells continues to be a source of controversy within environmental microbiology. This largely results from its notoriously unreliable performance record. In this article, we argue that the unpredictable nature of the approach comes from the initial strain selection step. Up until now, this has been dictated by the search for catabolically competent microorganisms, with little or no consideration given to other essential features that are required to be functionally active and persistent in target habitats. We describe how technical advances in molecular biology and analytical chemistry, now enable assessments of the functional diversity and spatial distribution of microbial communities to be made in situ. These advances now enable microbial populations, targeted for exploitation, to be differentiated to the cell level, an advance that is bound to improve microbial selection and exploitation. We argue that this information-based approach is already proving to be more effective than the traditional 'black-box' approach of strain selection. The future perspectives and opportunities for improving selection of effective microbial strains for bioaugmentation are also discussed.

Insight into pollutant bioavailability and toxicity using Raman confocal microscopy

Raman confocal microscopy was used to discriminate between cultures of Burkholderia xenovorans LB400 exposed to four different common environmental pollutants: phenanthrene, dodecane, 3-chlorobiphenyl and pentachlorophenol. Evidence is presented for the application of Raman spectroscopy as a bioassay for pollutant bioavailability and toxicity.

Chemotaxonomic identification of single bacteria by micro-Raman spectroscopy: application to clean-room-relevant biological contaminations

Microorganisms, such as bacteria, which might be present as contamination inside an industrial food or pharmaceutical clean room process need to be identified on short time scales in order to minimize possible health hazards as well as production downtimes causing financial deficits. Here we describe the first results of single-particle micro-Raman measurements in combination with a classification method, the so-called support vector machine technique, allowing for a fast, reliable, and nondestructive online identification method for single bacteria.

Micro-Raman spectroscopic identification of bacterial cells of the genus Staphylococcus and dependence on their cultivation conditions

Microbial contamination is not only a medical problem, but also plays a large role in pharmaceutical clean room production and food processing technology. Therefore many techniques were developed to achieve differentiation and identification of microorganisms. Among these methods vibrational spectroscopic techniques (IR, Raman and SERS) are useful tools because of their rapidity and sensitivity. Recently we have shown that micro-Raman spectroscopy in combination with a support vector machine is an extremely capable approach for a fast and reliable, non-destructive online identification of single bacteria belonging to different genera. In order to simulate different environmental conditions we analyzed in this contribution different Staphylococcus strains with varying cultivation conditions in order to evaluate our method with a reliable dataset. First, micro-Raman spectra of the bulk material and single bacterial cells that were grown under the same conditions were recorded and used separately for a distinct chemotaxonomic classification of the strains. Furthermore Raman spectra were recorded from single bacterial cells that were cultured under various conditions to study the influence of cultivation on the discrimination ability. This dataset was analyzed both with a hierarchical cluster analysis (HCA) and a support vector machine (SVM).