Mass Spectrometry Imaging of Complex Microbial Communities

Stable Isotope Labeling of Prodiginines and Serratamolides Produced by Serratia marcescens Directly on Agar and Simultaneous Visualization by Matrix-Assisted Laser Desorption/Ionization Imaging High-Resolution Mass Spectrometry

Matrix-assisted laser desorption/ionization imaging high-resolution mass spectrometry (MALDI-imaging-HRMS) is an important technique for visualizing the spatial distribution of compounds directly on the surface of organisms such as microorganisms, insects, plants, animals, and human tissues. However, MALDI-imaging-HRMS and the stable isotope labeling approach have never been combined for the detection and simultaneous visualization of labeled and unlabeled compounds, their analogues and derivatives, as well as their precursors. Herein, we present a methodology that labels microbial secondary metabolites directly on agar with stable isotopes and allows concurrent spatial distribution analyses by MALDI-imaging-HRMS. Using a thin film of labeled agar supplemented with [1-¹³C]-l-proline, [methyl-D₃]-l-methionine, ¹⁵NH₄Cl, or [¹⁵N]-l-serine overlaid on unlabeled agar, we demonstrate the incorporation of labeled precursors into prodiginines and serratamolides produced by an endophytic bacterium, Serratia marcescens, by MALDI-imaging-HRMS and HPLC-HRMS. Further, we show the incorporation of CD₃ into prodigiosin as well as its characteristic fragments directly by MALDI-imaging-HRMS². Our methodology has several advantages over currently existing techniques. First, both labeled and unlabeled compounds can be visualized simultaneously in high spatial resolution along with their labeled and unlabeled precursors. Second, by using a thin film of labeled agar, we utilize minimum amounts of expensive labeled compounds (1-3 mg) ensuring a cost-effective method for investigating biosynthetic pathways. Finally, our method allows in situ visualization and identification of target and nontarget compounds without the need of isolating the compounds. This is important for compounds that are produced by microorganisms in low, physiologically, or ecologically relevant concentrations.

Sample preparation for mass spectrometry imaging of leaf tissues: a case study on analyte delocalization

Appropriate sample preparation is pivotally important to obtain high-quality mass spectrometry imaging (MSI) data. Unlike mammalian tissues, preparation of cryosections from plant tissues for MSI measurement is quite challenging due to its intrinsic complex texture and cellular structure. This is especially true for leaf samples which are generally thin, water-rich, and fragile. In this work, a systematic study was performed, aiming to evaluate three embedding materials and five mounting approaches for matrix-assisted laser desorption ionization (MALDI) MSI of secondary metabolites in cross sections of the ginkgo leaf. Delocalization of endogenous metabolites was chosen as a major indicator for evaluation of three embedding materials including ice, carboxymethyl cellulose (CMC), and gelatin and different mounting approaches. Image distortion and analyte delocalization were observed when ice was used as an embedding medium. CMC embedding provided better results compared to the ice by using modified mounting approach. Among three embedding materials, no delocalization was observed in specimens embedded with gelatin, and gelatin embedding is the least affected by different mounting approaches. An alternative approach to mitigate analyte delocalization is the removal of embedding media embraced the tissue sections before mounting, which is particularly suitable for ice-embedded samples. Additionally, the extent of analyte delocalization was closely related to their lipophilicity/hydrophilicity properties, and less analyte diffusion was observed for hydrophobic analytes than for the water-soluble compounds.

Imaging the Microprocesses in Biofilm Matrices

Biofilms, which are aggregates of microorganisms and extracellular matrices, widely colonize natural water bodies, wastewater treatment systems, and body tissues, and have vital roles in water purification, biofouling, and infectious diseases. Recently, multiple imaging modalities have been developed to visualize the morphological structure and material distribution within biofilms and to probe the microprocesses in biofilm matrices, including biofilm formation, transfer and metabolism of substrates, and cell-cell communication. These technologies have improved our understanding of biofilm control and the fates of substrates in biofilms. In this review, we describe the principles of various imaging techniques and discuss the advantages and limitations of each approach to characterizing microprocesses in biofilm matrices.

Exploration of Fungal Metabolic Interactions Using Imaging Mass Spectrometry on Nanostructured Silicon

Application of matrix-assisted laser desorption/ionization imaging mass spectrometry to microbiology and natural product research has opened the door to the exploration of microbial interactions and the consequent discovery of new natural products and their functions in the interactions. However, several drawbacks of matrix-assisted laser desorption/ionization imaging mass spectrometry have limited its application especially to complicated and uneven microbial samples. Here, we applied nanostructured silicon as a substrate for surface-assisted laser desorption/ionization mass spectrometry for microbial imaging mass spectrometry to explore fungal metabolic interactions. We chose Phellinus noxius and Aspergillus strains to evaluate the potential of microbial imaging mass spectrometry on nanostructured silicon because both fungi produce a dense mass of aerial mycelia, which is known to complicate the collection of high-quality imaging mass spectrometry data. Our simple and straightforward sample imprinting method and low background interference resulted in an efficient analysis of small metabolites from the complex microbial interaction samples.

Imaging the Unimaginable: Desorption Electrospray Ionization - Imaging Mass Spectrometry (DESI-IMS) in Natural Product Research

Imaging mass spectrometry (IMS) has recently established itself in the field of "spatial metabolomics." Merging the sensitivity and fast screening of high-throughput mass spectrometry with spatial and temporal chemical information, IMS visualizes the production, location, and distribution of metabolites in intact biological models. Since metabolite profiling and morphological features are combined in single images, IMS offers an unmatched chemical detail on complex biological and microbiological systems. Thus, IMS-type "spatial metabolomics" emerges as a powerful and complementary approach to genomics, transcriptomics, and classical metabolomics studies. In this review, we summarize the current state-of-the-art IMS methods with a strong focus on desorption electrospray ionization (DESI)-IMS. DESI-IMS utilizes the original principle of electrospray ionization, but in this case solvent droplets are rastered and desorbed directly on the sample surface. The rapid and minimally destructive DESI-IMS chemical screening is achieved at ambient conditions and enables the accurate view of molecules in tissues at the µm-scale resolution. DESI-IMS analysis does not require complex sample preparation and allows repeated measurements on samples from different biological sources, including microorganisms, plants, and animals. Thanks to its easy workflow and versatility, DESI-IMS has successfully been applied to many different research fields, such as clinical analysis, cancer research, environmental sciences, microbiology, chemical ecology, and drug discovery. Herein we discuss the present applications of DESI-IMS in natural product research.

A Versatile Strategy for Characterization and Imaging of Drip Flow Microbial Biofilms

The inherent architectural and chemical complexities of microbial biofilms mask our understanding of how these communities form, survive, propagate, and influence their surrounding environment. Here we describe a simple and versatile workflow for the cultivation and characterization of model flow-cell-based microbial ecosystems. A customized low-shear drip flow reactor was designed and employed to cultivate single and coculture flow-cell biofilms at the air-liquid interface of several metal surfaces. Pseudomonas putida F1 and Shewanella oneidensis MR-1 were selected as model organisms for this study. The utility and versatility of this platform was demonstrated via the application of several chemical and morphological imaging techniques-including matrix-assisted laser desorption/ionization mass spectrometry imaging, secondary ion mass spectrometry imaging, and scanning electron microscopy-and through the examination of model systems grown on iron substrates of varying compositions. Implementation of these techniques in combination with tandem mass spectrometry and a two-step imaging principal component analysis strategy resulted in the identification and characterization of 23 lipids and 3 oligosaccharides in P. putida F1 biofilms, the discovery of interaction-specific analytes, and the observation of several variations in cell and substrate morphology present during microbially influenced corrosion. The presented workflow is well-suited for examination of both single and multispecies drip flow biofilms and offers a platform for fundamental inquiries into biofilm formation, microbe-microbe interactions, and microbially influenced corrosion.

Quantitative SIMS Imaging of Agar-Based Microbial Communities

After several decades of widespread use for mapping elemental ions and small molecular fragments in surface science, secondary ion mass spectrometry (SIMS) has emerged as a powerful analytical tool for molecular imaging in biology. Biomolecular SIMS imaging has primarily been used as a qualitative technique; although the distribution of a single analyte can be accurately determined, it is difficult to map the absolute quantity of a compound or even to compare the relative abundance of one molecular species to that of another. We describe a method for quantitative SIMS imaging of small molecules in agar-based microbial communities. The microbes are cultivated on a thin film of agar, dried under nitrogen, and imaged directly with SIMS. By use of optical microscopy, we show that the area of the agar is reduced by 26 ± 2% (standard deviation) during dehydration, but the overall biofilm morphology and analyte distribution are largely retained. We detail a quantitative imaging methodology, in which the ion intensity of each analyte is (1) normalized to an external quadratic regression curve, (2) corrected for isomeric interference, and (3) filtered for sample-specific noise and lower and upper limits of quantitation. The end result is a two-dimensional surface density image for each analyte. The sample preparation and quantitation methods are validated by quantitatively imaging four alkyl-quinolone and alkyl-quinoline N-oxide signaling molecules (including Pseudomonas quinolone signal) in Pseudomonas aeruginosa colony biofilms. We show that the relative surface densities of the target biomolecules are substantially different from values inferred through direct intensity comparison and that the developed methodologies can be used to quantitatively compare as many ions as there are available standards.

Advances in metabolome information retrieval: turning chemistry into biology. Part I: analytical chemistry of the metabolome

Metabolites are small molecules produced by enzymatic reactions in a given organism. Metabolomics or metabolic phenotyping is a well-established omics aimed at comprehensively assessing metabolites in biological systems. These comprehensive analyses use analytical platforms, mainly nuclear magnetic resonance spectroscopy and mass spectrometry, along with associated separation methods to gather qualitative and quantitative data. Metabolomics holistically evaluates biological systems in an unbiased, data-driven approach that may ultimately support generation of hypotheses. The approach inherently allows the molecular characterization of a biological sample with regard to both internal (genetics) and environmental (exosome, microbiome) influences. Metabolomics workflows are based on whether the investigator knows a priori what kind of metabolites to assess. Thus, a targeted metabolomics approach is defined as a quantitative analysis (absolute concentrations are determined) or a semiquantitative analysis (relative intensities are determined) of a set of metabolites that are possibly linked to common chemical classes or a selected metabolic pathway. An untargeted metabolomics approach is a semiquantitative analysis of the largest possible number of metabolites contained in a biological sample. This is part I of a review intending to give an overview of the state of the art of major metabolic phenotyping technologies. Furthermore, their inherent analytical advantages and limits regarding experimental design, sample handling, standardization and workflow challenges are discussed.

Visualization of Mycobacterial Biomarkers and Tuberculosis Drugs in Infected Tissue by MALDI-MS Imaging

MALDI mass-spectrometry imaging (MALDI-MSI) is a technique capable of the label-free identification and visualization of analytes in tissue sections. We have previously applied MALDI-MSI to the study of the spatial distribution of tuberculosis (TB) drugs in necrotic lung granulomas characteristic of pulmonary TB disease, revealing heterogeneous and often suboptimal drug distributions. To investigate the impact of differential drug distributions at sites of infection, we sought to image mycobacterial biomarkers to coregister drugs and bacteria in lesion sections. The traditional method of visualizing Mycobacterium tuberculosis inside lesions is acid-fast staining and microscopy. Directly analyzing and visualizing mycobacteria-specific lipid markers by MALDI-MSI provides detailed molecular information on bacterial distributions within granulomas, complementary to high-spatial-resolution staining and microscopy approaches. Moreover, spatial monitoring of molecular changes occurring in bacteria during granuloma development can potentially contribute to a greater understanding of pulmonary-TB pathogenesis. In this study, we developed a MALDI-MSI method to detect and visualize specific glycolipids of mycobacteria within TB lesions. The biomarker signal correlated well with the bacteria visualized by IHC and acid-fast staining. This observation was seen in samples collected from multiple animal models. Although individual bacteria could not be visualized because of the limit of spatial resolution (50 μm), bacterial clusters were clearly detected and heterogeneously distributed throughout lesions. The ability to visualize drugs, metabolites, and bacterial biomarkers by MALDI-MSI enabled direct colocalization of drugs with specific bacterial target populations (identifiable by distinct metabolic markers). Future applications include assessing drug activity in lesions by visualizing drug-mediated lipid changes and other drug-induced mycobacterial metabolic responses.

Microbial interactions trigger the production of antibiotics

Since the discovery of penicillin, antibiotics have been instrumental in treating infectious diseases. However, emerging antibiotic multi-resistance coinciding with a nearly exhausted drug pipeline is a major concern for the future of the therapy of infections. A novel approach for the discovery of antibiotics relies on the analysis of microbial consortia in their ecological context, taking into account the potential natural role of antibiotics. Co-cultivations of microorganisms have been successfully applied for the isolation of unknown secondary metabolites including antibiotics, and, thus, open new avenues to the production of bioactive compounds while at the same time providing insight into the natural function of the produced molecules and the regulation of their formation.

Homospermidine Lipids: A Compound Class Specifically Formed during Fruiting Body Formation of Myxococcus xanthus DK1622

The fascinating ability of myxobacteria to form multicellular spore filled fruiting bodies under starvation conditions was widely studied as a model for cooperative microbial behavior. The potential of a life cycle induced change of secondary metabolism, as a means to discover novel natural products, remains largely underexplored. We therefore studied the model organism Myxococcus xanthus DK1622 under submersed and solid cultivation conditions to find putatively life-cycle related compounds by applying statistical analysis on analytical data. Utilizing the advantageous characteristics of LC-MS, LC-MS/MS, and MALDI-MSI allowed the identification of compounds unambiguously associated with myxobacterial fruiting bodies. Our screening effort resulted in the purification and structure elucidation of a novel compound, the homospermidine lipid, from cultures that had undergone the fruiting process. A combination of molecular networking and targeted LC-MS/MS in conjunction with our in-house metabolomics database subsequently revealed alternative producers of the respective compound as well as a number of compounds belonging to the same structural class. Three further members of this compound class were isolated from an alternative producer and structurally elucidated by NMR. Insights into the biosynthesis of this novel compound class was gained by feeding of isotopically labeled substrates and in silico analysis.

Profiling of Microbial Colonies for High-Throughput Engineering of Multistep Enzymatic Reactions via Optically Guided Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry

Matrix-assisted laser desorption/ionization time-of-flight (MALDI-ToF) mass spectrometry (MS) imaging has been used for rapid phenotyping of enzymatic activities, but is mainly limited to single-step conversions. Herein we report a label-free method for high-throughput engineering of multistep biochemical reactions based on optically guided MALDI-ToF MS analysis of bacterial colonies. The bacterial cells provide containment of multiple enzymes and access to substrates and cofactors via metabolism. Automated MALDI-ToF MS acquisition from randomly distributed colonies simplifies procedures to prepare strain libraries without liquid handling. MALDI-ToF MS profiling was utilized to screen both substrate and enzyme libraries for natural product biosynthesis. Computational algorithms were developed to process and visualize the resulting mass spectral data sets. For analogues of the peptidic antibiotic plantazolicin, multivariate analyses by t-distributed stochastic neighbor embedding were used to group similar spectra for rapid identification of nonisobaric variants. After MALDI-ToF MS screening, follow-up analyses using high-resolution MS and tandem MS were readily performed on the same sample target. Separately, relative ion intensities of rhamnolipid congeners with various lipid moieties were evaluated to engineer enzymatic specificity. The glycolipid profiles of each colony were overlaid with optical images to facilitate the recovery of desirable mutants. For both the antibiotic and rhamnolipid cases, large populations of colonies were rapidly surveyed at the molecular level, providing information-rich insights not easily obtained with traditional screening assays. Utilizing standard microbiological techniques with routine microscopy and MALDI-ToF MS instruments, this simple yet effective workflow is applicable for a wide range of screening campaigns targeting multistep enzymatic reactions.