Exploration of inorganic C and N assimilation by soil microbes with time-of-flight secondary ion mass spectrometry

Mass spectrometry imaging in plants, microbes, and food: a review

Plant health, which affects the nutritional quality and safety of derivative food products, is influenced by symbiotic interactions with microorganisms. These interactions influence the local molecular profile at the tissue level. Therefore, studying the distribution of molecules within plants, microbes, and plant-based food is crucial to assess plant health, ensure the safety and quality of the agricultural products that become part of our food supply, and plan agricultural management practices. Within this framework, the molecular distribution within plant-based samples can be visualized with mass spectrometry imaging (MSI). This review describes key MSI methodologies, highlighting the role they play in unraveling the localization of metabolites, lipids, proteins, pigments, and elemental components across plants, microbes, and food products. Furthermore, investigations that involve multimodal molecular imaging approaches combining MSI with other imaging techniques are described. The advantages and limitations of the different MSI techniques that influence their applicability in diverse agro-food studies are described to enable informed choices for tailored analyses. For example, some MSI technologies involve meticulous sample preparation while others compromise spatial resolution to gain throughput. Key parameters such as sensitivity, ionization bias and fragmentation, reference database and compound class specificity are described and discussed in this review. With the ongoing refinements in instrumentation, data analysis, and integration of complementary techniques, MSI deepens our insight into the molecular biology of the agricultural ecosystem. This in turn empowers the quest for sustainable and productive agricultural practices.

Research progress of nano-scale secondary ion mass spectrometry (NanoSIMS) in soil science: Evolution, applications, and challenges

Nano-scale secondary ion mass spectrometry (NanoSIMS) has emerged as a powerful analytical tool for investigating various aspects of soils. In recent decades, the widespread adoption of advanced instrumentation and methods has contributed significantly to our understanding of organic-mineral assemblages. However, few literature reviews have comprehensively summarized NanoSIMS and its evolution, applications, limitations, and integration with other analytical techniques. In this review, we addressed this gap by comprehensively overviewing the development of NanoSIMS as an analytical tool in soils. This review covers studies on soil organic matter (SOM) cycling, soil-root interactions, and the behavior of metals, discussing the capability and limitations related to the distribution, composition, and interactions of various soil components that occur at mineral-organic interfaces. Furthermore, we examine recent advancements in high-resolution imaging and mass spectrometry technologies and their impact on the utilization of NanoSIMS in soils, along with potential new applications such as utilizing multiple ion beams and integrating them with other analytical techniques. The review emphasizes the importance of employing advanced techniques and methods to explore micro-interfaces and provide in situ descriptions of organic-mineral assemblages in future research. The ongoing development and refinement of NanoSIMS may yield new insights and breakthroughs in soil science, deepening our understanding of the intricate relationships between soil components and the processes that govern soil health and fertility.

Mass Spectral Imaging to Map Plant-Microbe Interactions

Plant-microbe interactions are of rising interest in plant sustainability, biomass production, plant biology, and systems biology. These interactions have been a challenge to detect until recent advancements in mass spectrometry imaging. Plants and microbes interact in four main regions within the plant, the rhizosphere, endosphere, phyllosphere, and spermosphere. This mini review covers the challenges within investigations of plant and microbe interactions. We highlight the importance of sample preparation and comparisons among time-of-flight secondary ion mass spectroscopy (ToF-SIMS), matrix-assisted laser desorption/ionization (MALDI), laser desorption ionization (LDI/LDPI), and desorption electrospray ionization (DESI) techniques used for the analysis of these interactions. Using mass spectral imaging (MSI) to study plants and microbes offers advantages in understanding microbe and host interactions at the molecular level with single-cell and community communication information. More research utilizing MSI has emerged in the past several years. We first introduce the principles of major MSI techniques that have been employed in the research of microorganisms. An overview of proper sample preparation methods is offered as a prerequisite for successful MSI analysis. Traditionally, dried or cryogenically prepared, frozen samples have been used; however, they do not provide a true representation of the bacterial biofilms compared to living cell analysis and chemical imaging. New developments such as microfluidic devices that can be used under a vacuum are highly desirable for the application of MSI techniques, such as ToF-SIMS, because they have a subcellular spatial resolution to map and image plant and microbe interactions, including the potential to elucidate metabolic pathways and cell-to-cell interactions. Promising results due to recent MSI advancements in the past five years are selected and highlighted. The latest developments utilizing machine learning are captured as an important outlook for maximal output using MSI to study microorganisms.

The Exploration of Microbial Natural Products and Metabolic Interaction Guided by Mass Spectrometry Imaging

As an impressive mass spectrometry technology, mass spectrometric imaging (MSI) can provide mass spectra data and spatial distribution of analytes simultaneously. MSI has been widely used in diverse fields such as clinical diagnosis, the pharmaceutical industry and environmental study due to its accuracy, high resolution and developing reproducibility. Natural products (NPs) have been a critical source of leading drugs; almost half of marketed drugs are derived from NPs or their derivatives. The continuous search for bioactive NPs from microorganisms or microbiomes has always been attractive. MSI allows us to analyze and characterize NPs directly in monocultured microorganisms or a microbial community. In this review, we briefly introduce current mainstream ionization technologies for microbial samples and the key issue of sample preparation, and then summarize some applications of MSI in the exploration of microbial NPs and metabolic interaction, especially NPs from marine microbes. Additionally, remaining challenges and future prospects are discussed.

Use of NanoSIMS to Identify the Lower Limits of Metabolic Activity and Growth by Serratia liquefaciens Exposed to Sub-Zero Temperatures

Serratia liquefaciens is a cold-adapted facultative anaerobic astrobiology model organism with the ability to grow at a Martian atmospheric pressure of 7 hPa. Currently there is a lack of data on its limits of growth and metabolic activity at sub-zero temperatures found in potential habitable regions on Mars. Growth curves and nano-scale secondary ion mass spectrometry (NanoSIMS) were used to characterize the growth and metabolic threshold for S. liquefaciens ATCC 27,592 grown at and below 0 °C. Cells were incubated in Spizizen medium containing three stable isotopes substituting their unlabeled counterparts; i.e., ¹³C-glucose, (¹⁵NH₄)₂SO₄, and H₂¹⁸O; at 0, −1.5, −3, −5, −10, or −15 °C. The isotopic ratios of ¹³C/¹²C, ¹⁵N/¹⁴N, and ¹⁸O/¹⁶O and their corresponding fractions were determined for 240 cells. NanoSIMS results revealed that with decreasing temperature the cellular amounts of labeled ions decreased indicating slower metabolic rates for isotope uptake and incorporation. Metabolism was significantly reduced at −1.5 and −3 °C, almost halted at −5 °C, and shut-down completely at or below −10 °C. While growth was observed at 0 °C after 5 days, samples incubated at −1.5 and −3 °C exhibited significantly slower growth rates until growth was detected at 70 days. In contrast, cell densities decreased by at least half an order of magnitude over 70 days in cultures incubated at ≤ −5 °C. Results suggest that S. liquefaciens, if transported to Mars, might be able to metabolize and grow in shallow sub-surface niches at temperatures above −5 °C and might survive—but not grow—at temperatures below −5 °C.

Mass Spectrometry Imaging of Complex Microbial Communities

In the two decades since mass spectrometry imaging (MSI) was first applied to visualize the distribution of peptides across biological tissues and cells, the technique has become increasingly effective and reliable. MSI excels at providing complementary information to existing methods for molecular analysis—such as genomics, transcriptomics, and metabolomics—and stands apart from other chemical imaging modalities through its capability to generate information that is simultaneously multiplexed and chemically specific. Today a diverse family of MSI approaches are applied throughout the scientific community to study the distribution of proteins, peptides, and small-molecule metabolites across many biological models.

The inherent strengths of MSI make the technique valuable for studying microbial systems. Many microbes reside in surface-attached multicellular and multispecies communities, such as biofilms and motile colonies, where they work together to harness surrounding nutrients, fend off hostile organisms, and shield one another from adverse environmental conditions. These processes, as well as many others essential for microbial survival, are mediated through the production and utilization of a diverse assortment of chemicals. Although bacterial cells are generally only a few microns in diameter, the ecologies they influence can encompass entire ecosystems, and the chemical changes that they bring about can occur over time scales ranging from milliseconds to decades. Because of their incredible complexity, our understanding of and influence over microbial systems requires detailed scientific evaluations that yield both chemical and spatial information. MSI is well-positioned to fulfill these requirements. With small adaptations to existing methods, the technique can be applied to study a wide variety of chemical interactions, including those that occur inside single-species microbial communities, between cohabitating microbes, and between microbes and their hosts.

In recognition of this potential for scientific advancement, researchers have adapted MSI methodologies for the specific needs of the microbiology research community. As a result, workflows exist for imaging microbial systems with many of the common MSI ionization methods. Despite this progress, there is substantial room for improvements in instrumentation, sample preparation, and data interpretation. This Account provides a brief overview of the state of technology in microbial MSI, illuminates selected applications that demonstrate the potential of the technique, and highlights a series of development challenges that are needed to move the field forward. In the coming years, as microbial MSI becomes easier to use and more universally applicable, the technique will evolve into a fundamental tool widely applied throughout many divisions of science, medicine, and industry.

Stable Isotope Probing Approaches to Study Anaerobic Hydrocarbon Degradation and Degraders

Stable isotope probing (SIP) techniques have become state-of-the-art in microbial ecology over the last 10 years, allowing for the targeted detection and identification of organisms, metabolic pathways and elemental fluxes active in specific processes within complex microbial communities. For studying anaerobic hydrocarbon-degrading microbial communities, four stable isotope techniques have been used so far: DNA/RNA-SIP, PLFA (phospholipid-derived fatty acids)-SIP, protein-SIP, and single-cell-SIP by nanoSIMS (nanoscale secondary ion mass spectrometry) or confocal Raman microscopy. DNA/RNA-SIP techniques are most frequently applied due to their most meaningful phylogenetic resolution. Especially using ¹³C-labeled benzene and toluene as model substrates, many new hydrocarbon degraders have been identified by SIP under various electron acceptor conditions. This has extended the current perspective of the true diversity of anaerobic hydrocarbon degraders relevant in the environment. Syntrophic hydrocarbon degradation was found to be a common mechanism for various electron acceptors. Fundamental concepts and recent advances in SIP are reflected here. A discussion is presented concerning how these techniques generate direct insights into intrinsic hydrocarbon degrader populations in environmental systems and how useful they are for more integrated approaches in the monitoring of contaminated sites and for bioremediation.

Heavy water and (15) N labelling with NanoSIMS analysis reveals growth rate-dependent metabolic heterogeneity in chemostats

To measure single-cell microbial activity and substrate utilization patterns in environmental systems, we employ a new technique using stable isotope labelling of microbial populations with heavy water (a passive tracer) and (15) N ammonium in combination with multi-isotope imaging mass spectrometry. We demonstrate simultaneous NanoSIMS analysis of hydrogen, carbon and nitrogen at high spatial and mass resolution, and report calibration data linking single-cell isotopic compositions to the corresponding bulk isotopic equivalents for Pseudomonas aeruginosa and Staphylococcus aureus. Our results show that heavy water is capable of quantifying in situ single-cell microbial activities ranging from generational time scales of minutes to years, with only light isotopic incorporation (∼0.1 atom % (2) H). Applying this approach to study the rates of fatty acid biosynthesis by single cells of S. aureus growing at different rates in chemostat culture (∼6 h, 1 day and 2 week generation times), we observe the greatest anabolic activity diversity in the slowest growing populations. By using heavy water to constrain cellular growth activity, we can further infer the relative contributions of ammonium versus amino acid assimilation to the cellular nitrogen pool. The approach described here can be applied to disentangle individual cell activities even in nutritionally complex environments.

Revisiting N₂ fixation in Guerrero Negro intertidal microbial mats with a functional single-cell approach

Photosynthetic microbial mats are complex, stratified ecosystems in which high rates of primary production create a demand for nitrogen, met partially by N₂ fixation. Dinitrogenase reductase (nifH) genes and transcripts from Cyanobacteria and heterotrophic bacteria (for example, Deltaproteobacteria) were detected in these mats, yet their contribution to N2 fixation is poorly understood. We used a combined approach of manipulation experiments with inhibitors, nifH sequencing and single-cell isotope analysis to investigate the active diazotrophic community in intertidal microbial mats at Laguna Ojo de Liebre near Guerrero Negro, Mexico. Acetylene reduction assays with specific metabolic inhibitors suggested that both sulfate reducers and members of the Cyanobacteria contributed to N₂ fixation, whereas (15)N₂ tracer experiments at the bulk level only supported a contribution of Cyanobacteria. Cyanobacterial and nifH Cluster III (including deltaproteobacterial sulfate reducers) sequences dominated the nifH gene pool, whereas the nifH transcript pool was dominated by sequences related to Lyngbya spp. Single-cell isotope analysis of (15)N₂-incubated mat samples via high-resolution secondary ion mass spectrometry (NanoSIMS) revealed that Cyanobacteria were enriched in (15)N, with the highest enrichment being detected in Lyngbya spp. filaments (on average 4.4 at% (15)N), whereas the Deltaproteobacteria (identified by CARD-FISH) were not significantly enriched. We investigated the potential dilution effect from CARD-FISH on the isotopic composition and concluded that the dilution bias was not substantial enough to influence our conclusions. Our combined data provide evidence that members of the Cyanobacteria, especially Lyngbya spp., actively contributed to N₂ fixation in the intertidal mats, whereas support for significant N₂ fixation activity of the targeted deltaproteobacterial sulfate reducers could not be found.

Emerging mass spectrometry techniques for the direct analysis of microbial colonies

One of the emerging areas in microbiology is detecting specialized metabolites produced by microbial colonies and communities with mass spectrometry. In this review/perspective, we illustrate the emerging mass spectrometry methodologies that enable the interrogation of specialized metabolites directly from microbial colonies. Mass spectrometry techniques such as imaging mass spectrometry and real-time mass spectrometry allow two and three-dimensional visualization of the distribution of metabolites, often with minimal sample pretreatment. The speed in which molecules are captured using these methods requires the development of new molecular visualization tools such as molecular networking. Together, these tools are beginning to provide unprecedented insight into the chemical world that microbes experience.

An underground tale: contribution of microbial activity to plant iron acquisition via ecological processes

BACKGROUND

Iron (Fe) deficiency in crops is a worldwide agricultural problem. Plants have evolved several strategies to enhance Fe acquisition, but increasing evidence has shown that the intrinsic plant-based strategies alone are insufficient to avoid Fe deficiency in Fe-limited soils. Soil micro-organisms also play a critical role in plant Fe acquisition; however, the mechanisms behind their promotion of Fe acquisition remain largely unknown.

SCOPE

This review focuses on the possible mechanisms underlying the promotion of plant Fe acquisition by soil micro-organisms.

CONCLUSIONS

Fe-deficiency-induced root exudates alter the microbial community in the rhizosphere by modifying the physicochemical properties of soil, and/or by their antimicrobial and/or growth-promoting effects. The altered microbial community may in turn benefit plant Fe acquisition via production of siderophores and protons, both of which improve Fe bioavailability in soil, and via hormone generation that triggers the enhancement of Fe uptake capacity in plants. In addition, symbiotic interactions between micro-organisms and host plants could also enhance plant Fe acquisition, possibly including: rhizobium nodulation enhancing plant Fe uptake capacity and mycorrhizal fungal infection enhancing root length and the nutrient acquisition area of the root system, as well as increasing the production of Fe(3+) chelators and protons.

A multi-scale approach to determine accurate elemental and isotopic ratios by nano-scale secondary ion mass spectrometry imaging

RATIONALE

Nano-scale secondary ion mass spectrometry (NanoSIMS) is still hampered by a lack of appropriate calibration method for the quantification of elemental and isotopic ratios in heterogeneous materials such as soil samples. The potential of (13)C-(15)N-labeled density fractions of soil to calibrate the C/N, (13)C/(12)C and (15)N/(14)N ratios provided by NanoSIMS was evaluated.

METHODS

The spatial organization of soil particles found at the macro- and micro-scales were compared. The C/N, (13)C/(12)C and (15)N/(14)N ratios measured at the macroscopic scale from different density fractions using an elemental analyzer coupled to an isotope ratio mass spectrometer (EA/IRMS) were compared with the corresponding micro-scale NanoSIMS measurements. When the macro- and micro-scales patterns were similar, macroscopic scale measurements obtained by EA/IRMS and the corresponding NanoSIMS C/N and (15)N/(14)N ratios averaged per fraction were used to obtain correction equations. The correction method using the internal calibration procedure was compared with the traditional one using a single organic standard.

RESULTS

It was demonstrated that the correction method using an internal calibration procedure was applicable for NanoSIMS images acquired on more than 500 µm(2) per fraction and provided more accurate C/N and (15)N/(14)N ratios than the traditional correction method.

CONCLUSIONS

As long as the NanoSIMS sampling was representative of the macroscopic properties, the correction method using an internal calibration procedure allowed better quantification of the isotope tracers and characterization of the C/N ratios. This method not only produced qualitative images, but also accurate quantitative parameters from which ecological interpretations can be derived.

Imaging mass spectrometry in microbiology

Imaging mass spectrometry tools allow the two-dimensional visualization of the distribution of trace metals, metabolites, surface lipids, peptides and proteins directly from biological samples without the need for chemical tagging or antibodies, and are becoming increasingly useful for microbiology applications. These tools, comprising different imaging mass spectrometry techniques, are ushering in an exciting new era of discovery by enabling the generation of chemical hypotheses based on the spatial mapping of atoms and molecules that can correlate to or transcend observed phenotypes. In this Innovation article, we explore the wide range of imaging mass spectrometry techniques that is available to microbiologists and describe the unique applications of these tools to microbiology with respect to the types of samples to be investigated.

A composite biochemical system for bacterial nitrate and nitrite assimilation as exemplified by Paracoccus denitrificans

The denitrifying bacterium Paracoccus denitrificans can grow aerobically or anaerobically using nitrate or nitrite as the sole nitrogen source. The biochemical pathway responsible is expressed from a gene cluster comprising a nitrate/nitrite transporter (NasA), nitrite transporter (NasH), nitrite reductase (NasB), ferredoxin (NasG) and nitrate reductase (NasC). NasB and NasG are essential for growth with nitrate or nitrite as the nitrogen source. NADH serves as the electron donor for nitrate and nitrite reduction, but only NasB has a NADH-oxidizing domain. Nitrate and nitrite reductase activities show the same Km for NADH and can be separated by anion-exchange chromatography, but only fractions containing NasB retain the ability to oxidize NADH. This implies that NasG mediates electron flux from the NADH-oxidizing site in NasB to the sites of nitrate and nitrite reduction in NasC and NasB respectively. Delivery of extracellular nitrate to NasBGC is mediated by NasA, but both NasA and NasH contribute to nitrite uptake. The roles of NasA and NasC can be substituted during anaerobic growth by the biochemically distinct membrane-bound respiratory nitrate reductase (Nar), demonstrating functional overlap. nasG is highly conserved in nitrate/nitrite assimilation gene clusters, which is consistent with a key role for the NasG ferredoxin, as part of a phylogenetically widespread composite nitrate and nitrite reductase system.

In situ mapping of nutrient uptake in the rhizosphere using nanoscale secondary ion mass spectrometry

Plant roots and microorganisms interact and compete for nutrients within the rhizosphere, which is considered one of the most biologically complex systems on Earth. Unraveling the nitrogen (N) cycle is key to understanding and managing nutrient flows in terrestrial ecosystems, yet to date it has proved impossible to analyze and image N transfer in situ within such a complex system at a scale relevant to soil-microbe-plant interactions. Linking the physical heterogeneity of soil to biological processes marks a current frontier in plant and soil sciences. Here we present a new and widely applicable approach that allows imaging of the spatial and temporal dynamics of the stable isotope (15)N assimilated within the rhizosphere. This approach allows visualization and measurement of nutrient resource capture between competing plant cells and microorganisms. For confirmation we show the correlative use of nanoscale secondary ion mass spectrometry, and transmission electron microscopy, to image differential partitioning of (15)NH(4)(+) between plant roots and native soil microbial communities at the submicron scale. It is shown that (15)N compounds can be detected and imaged in situ in individual microorganisms in the soil matrix and intracellularly within the root. Nanoscale secondary ion mass spectrometry has potential to allow the study of assimilatory processes at the submicron level in a wide range of applications involving plants, microorganisms, and animals.

Single-cell ecophysiology of microbes as revealed by Raman microspectroscopy or secondary ion mass spectrometry imaging

An astonishing diversity of microorganisms thrives on our planet and their activities are fundamental for the functioning of all ecosystems including the human body. Consequently, detailed insights into the functions performed by microorganisms in their natural environment are required to understand human biology and the biology of the world around us and to lay the foundations for targeted manipulation of microbial communities. Isotope-labeling techniques combined with molecular detection tools are frequently used by microbial ecologists to directly link structure and function of microbial communities and to monitor metabolic properties of uncultured microbes at the single-cell level. However, only the recent combination of such techniques with Raman microspectroscopy or secondary ion mass spectrometry enables functional studies of microbes on a single-cell level by using stable isotopes as labels. This review provides an overview of these new techniques and their applications in microbial ecology, which allow us to investigate the ecophysiology of uncultured microbes to an extent that was unimaginable just a few years ago.

Geobiological investigations using secondary ion mass spectrometry: microanalysis of extant and paleo-microbial processes

The application of secondary ion mass spectrometry (SIMS) has tremendous value for the field of geobiology, representing a powerful tool for identifying the specific role of micro-organisms in biogeochemical cycles. In this review, we highlight a number of diverse applications for SIMS and nanoSIMS in geobiological research. SIMS performs isotope and elemental analysis at microscale enabling the investigation of the physiology of individual microbes within complex communities. Additionally, through the study of isotopic or chemical characteristics that are common in both living and ancient microbial communities, SIMS allows for direct comparisons of potential biosignatures derived from extant microbial cells and their fossil equivalents.

Patterns of 15N assimilation and growth of methanotrophic ANME-2 archaea and sulfate-reducing bacteria within structured syntrophic consortia revealed by FISH-SIMS

Methane release from the oceans is controlled in large part by syntrophic interactions between anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria (DSS), frequently found as organized consortia. An understanding of the specifics of this symbiotic relationship and the metabolic heterogeneity existing between and within individual methane-oxidizing aggregates is currently lacking. Here, we use the microanalytical method FISH-SIMS (fluorescence in situ hybridization-secondary ion mass spectrometry) to describe the physiological traits and anabolic activity of individual methanotrophic consortia, specifically tracking (15)N-labelled protein synthesis to examine the effects of organization and size on the metabolic activity of the syntrophic partners. Patterns of (15)N distribution within individual aggregates showed enhanced (15)N assimilation in ANME-2 cells relative to the co-associated DSS revealing a decoupling in anabolic activity between the partners. Protein synthesis in ANME-2 cells was sustained throughout the core of individual ANME-2/DSS consortia ranging in size range from 4 to 20 μm. This indicates that metabolic activity of the methane-oxidizing archaea is not limited to, or noticeably enhanced at the ANME-2/DSS boundary. Overall, the metabolic activity of both syntrophic partners within consortia was greater than activity measured in representatives of the ANME-2 and DSS observed alone, with smaller ANME-2/DSS aggregates displaying a tendency for greater (15)N uptake and doubling times ranging from 3 to 5 months. The combination of (15)N-labelling and FISH-SIMS provides an important perspective on the extent of heterogeneity within methanotrophic aggregates and may aid in constraining predictive models of activity and growth by these syntrophic consortia.

Dynamic secondary ion mass spectrometry imaging of microbial populations utilizing C-labelled substrates in pure culture and in soil

We demonstrate that dynamic secondary ion mass spectrometry (SIMS)-based ion microscopy can provide a means of measuring (13)C assimilation into individual bacterial cells grown on (13)C-labelled organic compounds in the laboratory and in field soil. We grew pure cultures of Pseudomonas putida NCIB 9816-4 in minimal media with known mixtures of (12)C- and (13)C-glucose and analysed individual cells via SIMS imaging. Individual cells yielded signals of masses 12, 13, 24, 25, 26 and 27 as negative secondary ions indicating the presence of (12)C(-), (13)C(-), (24)((12)C(2))(-), (25)((12)C(13)C)(-), (26)((12)C(14)N)(-) and (27)((13)C(14)N)(-) ions respectively. We verified that ratios of signals taken from the same cells only changed minimally during a approximately 4.5 min period of primary O(2)(+) beam sputtering by the dynamic SIMS instrument in microscope detection mode. There was a clear relationship between mass 27 and mass 26 signals in Pseudomonas putida cells grown in media containing varying proportions of (12)C- to (13)C-glucose: a standard curve was generated to predict (13)C-enrichment in unknown samples. We then used two strains of Pseudomonas putida able to grow on either all or only a part of a mixture of (13)C-labelled and unlabelled carbon sources to verify that differential (13)C signals measured by SIMS were due to (13)C assimilation into cell biomass. Finally, we made three key observations after applying SIMS ion microscopy to soil samples from a field experiment receiving (12)C- or (13)C-phenol: (i) cells enriched in (13)C were heterogeneously distributed among soil populations; (ii) (13)C-labelled cells were detected in soil that was dosed a single time with (13)C-phenol; and (iii) in soil that received 12 doses of (13)C-phenol, 27% of the cells in the total community were more than 90% (13)C-labelled.

A single-cell view on the ecophysiology of anaerobic phototrophic bacteria

Quantitative information on the ecophysiology of individual microorganisms is generally limited because it is difficult to assign specific metabolic activities to identified single cells. Here, we develop and apply a method, Halogen In Situ Hybridization-Secondary Ion Mass Spectroscopy (HISH-SIMS), and show that it allows simultaneous phylogenetic identification and quantitation of metabolic activities of single microbial cells in the environment. Using HISH-SIMS, individual cells of the anaerobic, phototropic bacteria Chromatium okenii, Lamprocystis purpurea, and Chlorobium clathratiforme inhabiting the oligotrophic, meromictic Lake Cadagno were analyzed with respect to H(13)CO(3)(-) and (15)NH(4)(+) assimilation. Metabolic rates were found to vary greatly between individual cells of the same species, showing that microbial populations in the environment are heterogeneous, being comprised of physiologically distinct individuals. Furthermore, C. okenii, the least abundant species representing approximately 0.3% of the total cell number, contributed more than 40% of the total uptake of ammonium and 70% of the total uptake of carbon in the system, thereby emphasizing that numerically inconspicuous microbes can play a significant role in the nitrogen and carbon cycles in the environment. By introducing this quantification method for the ecophysiological roles of individual cells, our study opens a variety of possibilities of research in environmental microbiology, especially by increasing the ability to examine the ecophysiological roles of individual cells, including those of less abundant and less active microbes, and by the capacity to track not only nitrogen and carbon but also phosphorus, sulfur, and other biological element flows within microbial communities.

Subsurface biomolecular imaging of Streptomyces coelicolor using secondary ion mass spectrometry

Imaging using time-of-flight secondary ion mass spectrometry (TOF-SIMS) with buckministerfullerene (C(60)) primary ions offers the possibility of mapping the chemical distribution of molecular species from biological surfaces. Here we demonstrate the capability of the technique to provide biomolecular information from the cell surface as well as from within the surface, as illustrated with the distribution of two antibiotics in Streptomyces coelicolor (a mycelial bacterium). Differential production of the two pigmented antibiotics under salt-stressed and normal conditions in submerged cultivations could be detected from the TOF-SIMS spectra of the bacteria, demonstrating the potential of the technique in studying microbial physiology. Although both the antibiotics were detected on the cell surface, sputter etching with C(60)(+) revealed the spectral features of only one of the antibiotics within the cells. Exploratory analysis of the images using principal component analysis assisted in analyzing the spectral information with respect to peak contributions and their spatial distributions. The technique allows the study of not only lateral but also the depthwise distribution of biomolecules, uniquely enabling exploration of the processes within biological systems with minimal system intervention and with little a priori biochemical knowledge of relevance.

Visualization, modelling and prediction in soil microbiology

The introduction of new approaches for characterizing microbial communities and imaging soil environments has benefited soil microbiology by providing new ways of detecting and locating microorganisms. Consequently, soil microbiology is poised to progress from simply cataloguing microbial complexity to becoming a systems science. A systems approach will enable the structures of microbial communities to be characterized and will inform how microbial communities affect soil function. Systems approaches require accurate analyses of the spatio-temporal properties of the different microenvironments present in soil. In this Review we advocate the need for the convergence of the experimental and theoretical approaches that are used to characterize and model the development of microbial communities in soils.

Microbial proteomics: a mass spectrometry primer for biologists

It is now more than 10 years since the publication of the first microbial genome sequence and science is now moving towards a post genomic era with transcriptomics and proteomics offering insights into cellular processes and function. The ability to assess the entire protein network of a cell at a given spatial or temporal point will have a profound effect upon microbial science as the function of proteins is inextricably linked to phenotype. Whilst such a situation is still beyond current technologies rapid advances in mass spectrometry, bioinformatics and protein separation technologies have produced a step change in our current proteomic capabilities. Subsequently a small, but steadily growing, number of groups are taking advantage of this cutting edge technology to discover more about the physiology and metabolism of microorganisms. From this research it will be possible to move towards a systems biology understanding of a microorganism. Where upon researchers can build a comprehensive cellular map for each microorganism that links an accurately annotated genome sequence to gene expression data, at a transcriptomic and proteomic level.In order for microbiologists to embrace the potential that proteomics offers, an understanding of a variety of analytical tools is required. The aim of this review is to provide a basic overview of mass spectrometry (MS) and its application to protein identification. In addition we will describe how the protein complexity of microbial samples can be reduced by gel-based and gel-free methodologies prior to analysis by MS. Finally in order to illustrate the power of microbial proteomics a case study of its current application within the Bacilliaceae is given together with a description of the emerging discipline of metaproteomics.

A novel method for the study of the biophysical interface in soils using nano-scale secondary ion mass spectrometry

The spatial location of microorganisms and their activity within the soil matrix have major impacts on biological processes such as nutrient cycling. However, characterizing the biophysical interface in soils is hampered by a lack of techniques at relevant scales. A novel method for studying the distribution of microorganisms that have incorporated isotopically labelled substrate ('active' microorganisms) in relation to the soil microbial habitat is provided by nano-scale secondary ion mass spectrometry (NanoSIMS). Pseudomonas fluorescens are ubiquitous in soil and were therefore used as a model for 'active' microorganisms in soil. Batch cultures (NCTC 10038) were grown in a minimal salt medium containing 15N-ammonium sulphate (15/14N ratio of 1.174), added to quartz-based white sand or soil (coarse textured sand), embedded in Araldite 502 resin and sectioned for NanoSIMS analysis. The 15N-enriched P. fluorescens could be identified within the soil structure, demonstrating that the NanoSIMS technique enables the study of spatial location of microbial activity in relation to the heterogeneous soil matrix. This technique is complementary to the existing techniques of digital imaging analysis of soil thin sections and scanning electron microscopy. Together with advanced computer-aided tomography of soils and mathematical modelling of soil heterogeneity, NanoSIMS may be a powerful tool for studying physical and biological interactions, thereby furthering our understanding of the biophysical interface in soils.

Identifying the Characteristic Secondary Ions of Lignin Polymer Using ToF−SIMS

The chemical structure of lignin, a complex, irregular polymer of phenylpropane units that occurs in plant cell walls, was investigated using time-of-flight secondary ion mass spectrometry (ToF-SIMS). The positive ToF-SIMS spectra of lignin isolated from pine and beech wood showed prominent secondary ions possessing guaiacyl (at m/z 137 and 151) or syringyl (at m/z 167 and 181) rings, which are the basic building units of lignin polymer. This shows that ToF-SIMS is a useful tool for lignin structural analysis. The peaks at m/z 137 and 167 were assigned as the C6-C1 ion, and the peaks at m/z 151 and 181 may be double-component, the C6-C1 ion and the C6-C2 ion. We confirmed the characteristic guaiacyl ions using a synthetic lignin model compound, dehydrogenation polymer (DHP), which was formed by polymerizing of unlabeled and deuterium-labeled coniferyl alcohols. The formation mechanism of the main secondary ions was deduced by labeling specific positions of coniferyl alcohols with a stable isotope to study the relationship between chemical structure and secondary ion formation in ToF-SIMS.

Measure of carbon and nitrogen stable isotope ratios in cultured cells

We report the measurement of the natural isotope ratios of nitrogen and carbon in subcellular volumes of individual cells among a population of cultured cells using a multi-isotope imaging mass spectrometer (MIMS), [MIMS is the prototype of the NanoSIMS 50, Cameca, France.] We also measured the nitrogen and carbon isotope ratio in cells after they had been cultured in media enriched with the amino acid glycine labeled with either 13C or 15N. The results demonstrate that 13C/12C and 15N/14N isotope ratios can be measured directly on a subcellular scale. This opens the way for the use of stable isotopes, in particular 15N, as labels to measure the intracellular turnover of biomolecules. Such a capability should help resolve a wide range of biomedical problems.

Filamentous fungi: the indeterminate lifestyle and microbial ecology

The filamentous fungi have dynamic and variable hyphal structures within which cytoplasm can be moved, synthesized, and degraded, in response to changes in environmental conditions, resource availability, and resource distribution. Their study has gone through several phases. In the first phase, direct observation was emphasized without undue concern for interior structures or in the presence of cytoplasm. By the mid-1970s, single biochemical proxies (ergosterol, marker fatty acids, chitin derivatives, etc.) were being used increasingly. The use of these surrogate single measurements continues, in spite of their inability to provide information on the physical structure of the filamentous fungi. Molecular approaches also are being used, primarily through the use of bulk nucleic acid extraction and cloning. Because the sources of the nucleic acids used in such studies usually are not known, taxonomic and phylogenetic information derived by this approach cannot be linked to specific fungal structures. Recently, a greater emphasis has been placed on assessing physical aspects of indeterminate fungal growth, involving the assessment of cytoplasm-filled and evacuated (empty) hyphae. Both of these parameters are important for describing filamentous fungal growth and function. The use of phase contrast microscopy and varied general stains, as well as fluorogenic substrates with observation by epifluorescence microscopy, has made it possible to provide estimates of cytoplasm-filled hyphal lengths. Using this approach, it has been possible to evaluate the responses of the indeterminate fungal community to changes in environmental conditions, including soil management. It is now possible to obtain molecular information from individual bacteria and fungal structures (hyphae, spores, fruiting bodies) recovered from environments, making it possible to link individual fungal structures with their taxonomic and phylogenetic information. In addition, this information can be considered in the context of the indeterminate filamentous fungal lifestyle, involving the dynamics of resource allocation to hyphal structural development and synthesis of cytoplasm. Use of this approach should make it possible to gain a greater appreciation of the indeterminate filamentous fungal lifestyle, particularly in the context of microbial ecology.