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Isothermal titration calorimetry combined with surface complexation modeling is an ideal technique to provide further characterization of microbial surface reactivity towards protons and metal ions. This technique can produce enthalpies of protonation and metal ion coordination of acidic functional groups on microbial surfaces. This information is critical for understanding the thermodynamic driving force of surface complexation and provides key information for the indirect identification of surface ligands. Topics covered in this chapter include how this technique complements traditional methods of microbial surface reactivity, necessary system characterization prior to performing calorimetric experiments, how to prepare biomass and solutions for calorimetric titrations, difficult aspects of this technique, and data analysis and interpretation.
Scanning probe microscopy (SPM) is a suite of related imaging methods, in which variations in the interaction force between a probe and a sample surface are used to generate image contrast. These instruments are incredibly sensitive; they can measure forces on the order of those required to break physical and chemical bonds, and under the most optimal conditions, atomic-scale resolution can be achieved. Although SPM is still primarily used for imaging, it is increasingly being used to measure nanoscale properties and interaction forces. This chapter serves as an introduction to the fundamentals of SPM and to the most prevalent methods needed for the investigation of mineral–microbe interactions.
Potentiometric titrations are a widely used technique to quantify proton-active functional groups on microorganisms, their exudates, biominerals, and biofilms. In this chapter, we provide a step-by-step introduction to the preparation of microbial cells for the determination of proton buffering capacity using modern autotitration systems. Following a discussion of how to process titration data and plot titration curves, we review commonly used thermodynamic approaches to model titration curves in order to calculate cell wall functional group acidity constants and corresponding site concentrations. In geomicrobiology, protonation models are primarily used as a basis for the development of surface complexation models that can predict the adsorption of charged species such as metals to biomass. The case example that follows outlines the development of a surface complexation model for the adsorption of cadmium to a species of the marine cyanobacterium Synechococcus, using a protonation model developed from titration data as its basis. In the last section, we introduce the reader to other analytical tools that are complementary to titration results, and discuss a few common complications to the titration approach when it is applied to natural materials.
X-ray diffraction techniques provide information regarding the formation and alteration of mineral phases that is critical for assessing geomicrobial processes. Of particular interest is the use of powder X-ray diffraction (pXRD) to identify unknown solid-state materials, determine the particle size of nanoscale mineral phases, and refine structure characteristics, such as unit cell parameters and atomic positions. The goal of this chapter is to provide practical knowledge for the successful preparation of solid mineral samples, optimal data collection strategies, and analysis of diffractograms collected from pXRD experiments. Specific uses of pXRD techniques in geomicrobiology are discussed to demonstrate the importance of diffraction in advancing our understanding of microbial communities in geologic systems.
Lipid biomarker analysis is a useful tool for characterizing microbial communities in geomicrobiology. Phospholipid fatty acids (PLFA) are major components of microbial membranes, and analysis of these markers provides insight into microbial biomass, community structure, and metabolic processes. This article reviews the methods for extraction, fractionation, derivatization, and quantification of PLFA, as well as the interpretation of PLFA patterns for microbial community analysis in natural environmental systems. The discussion centers on the development, the subsequent modifications, and the advantages and limitations of the methods. Two case studies are given to illustrate the applications of intact phospholipid profiling (IPP) and PLFA in geomicrobiology. The recent developments and future directions of microbial signature lipid analysis are also discussed.
Geomicrobiological investigations benefit from knowledge of geochemical and biological systems at different scales, including information about both the abiotic and the biotic components. Gathering this information requires analysis and characterization of both abiotic and biotic components of the target system. The techniques presented in this chapter were selected to cover a variety of needs in geomicrobiological studies, including general sample collection and storage, organic and inorganic compound quantification, and best practices for cultivation, observation, and analysis of microorganisms and microbial communities. In this chapter, introductions and discussions for common techniques provide the reader with a basic understanding of the technique itself, which samples can be analyzed using the technique, and how to prepare samples for analysis. Detailed methods are provided for select techniques, and citations to standard methods are provided for techniques whenever available. For techniques that are rapidly evolving, recent developments and applications are discussed.
Geomicrobiology is the study of microbes and microbial processes and their role in driving environmental and geological processes at scales ranging from the nano, micron, to meter scale. This growing field has seen major advances in recent years, largely due to the development of new analytical tools and improvements to existing techniques, which allow us to better understand the complex interactions between microbes and their surroundings. In this comprehensive handbook, expert authors outline the state-of-the-art and emerging analytical techniques used in geomicrobiology. Readers are guided through each technique including background theory, sample preparation, standard methodology, data collection and analysis, best practices and common pitfalls, and examples of how and where the technique has been applied. The book provides a practical go-to reference for advanced students, researchers and professional scientists looking to employ techniques commonly used in geomicrobiology.
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