9 The Extraction and Identification of Respiratory Lipoquinones of Prokaryotes and Their Use in Taxonomy
Publication date: 2011 Source:Methods in Microbiology, Volume 38 Author(s): Milton S. da Costa , Luciana Albuquerque , M. Fernanda Nobre , Robin Wait Isoprenol quinone identification is used to complement fatty acid composition, polar lipid patterns and, in some cases, determination of the peptidoglycan type as part of the chemotaxonomic characterization of prokaryotes. Although the results are not usually discriminatory at the species level, they provide valuable data at higher taxonomic levels. We will give some examples of the value of the isoprenoid quinone analysis and describe the methods that can be used in ...
Source: Methods in Microbiology - October 12, 2014 Category: Microbiology Source Type: research
8 The Identification of Fatty Acids in Bacteria
Publication date: 2011 Source:Methods in Microbiology, Volume 38 Author(s): Milton S. da Costa , Luciana Albuquerque , M. Fernanda Nobre , Robin Wait The fatty acid composition is probably the most important chemotaxonomic parameter used for the differentiation of prokaryote taxa at the species level because it correlates very well with the accepted DNA:DNA hybridization-based species concept of many groups of bacteria. However, care must be taken to standardize the conditions of growth as well as those of the gas chromatography. If these standardized conditions are followed, valuable information may be acquired fr...
Source: Methods in Microbiology - October 12, 2014 Category: Microbiology Source Type: research
7 The Identification of Polar Lipids in Prokaryotes
Publication date: 2011 Source:Methods in Microbiology, Volume 38 Author(s): Milton S. da Costa , Luciana Albuquerque , M. Fernanda Nobre , Robin Wait Prokaryotes possess an enormous variety of polar lipids, primarily phospholipids and glycolipids, that cannot be easily identified at the chemical level. However, by using thin-layer chromatography, these polar lipids have been shown to constitute important chemotaxonomic parameters that can aid in the characterization of new taxa. The analysis of polar lipids is recommended for the description of new taxa because these lipids can be used to confirm the taxonomic affi...
Source: Methods in Microbiology - October 12, 2014 Category: Microbiology Source Type: research
6 Cell Wall Teichoic Acids in the Taxonomy and Characterization of Gram-positive Bacteria††Dedicated to the memory of Professor L.V. Backinowsky (1938–2011) – friend and colleague, whose inspiration and insight problems contributed to the writing of this chapter.
Publication date: 2011 Source:Methods in Microbiology, Volume 38 Author(s): Natal’ya V. Potekhina , Galina M. Streshinskaya , Elena M. Tul'skaya , Alexander S. Shashkov The use of cell wall teichoic acids as chemotaxonomic markers in the systematics of members of the order Actinomycetales and the genus Bacillus is discussed. Numerous examples show that these polymers are species-specific for representatives of the genera Actinomadura, Agromyces, Brevibacterium, Glycomyces, Nocardioides, Nocardiopsis, Nonomuraea, Streptomyces, and type strains of the B. subtilis group. The structural diversity and abundance of suc...
Source: Methods in Microbiology - October 12, 2014 Category: Microbiology Source Type: research
5 Peptidoglycan Structure
Publication date: 2011 Source:Methods in Microbiology, Volume 38 Author(s): Peter Schumann Information on the peptidoglycan structure is an indispensable component for the description of new genera of Gram-positive bacteria. In certain genera, structural variations of the peptidoglycan support even the differentiation at the species level. The analysis of the peptidoglycan requires the isolation and purification of this three-dimensionally cross-linked polymer, a set of analytical techniques to identify and to quantify its components as well as specific knowledge on how to conclude structural information from the data...
Source: Methods in Microbiology - October 12, 2014 Category: Microbiology Source Type: research
4 Microscopy
Publication date: 2011 Source:Methods in Microbiology, Volume 38 Author(s): Manfred Rohde In this chapter, the emphasis is placed on light microscopic examinations of unstained and stained specimens, as well as preparation protocols for transmission electron microscopy (TEM) and field emission scanning electron microscopy (FESEM), with the intention to provide a concise hands-on guide for scientists who would gather information about the structure of microorganisms using light and electron microscopic techniques. First, illuminating modes in light microscopic examination of microorganisms are described, followed by pr...
Source: Methods in Microbiology - October 12, 2014 Category: Microbiology Source Type: research
3 Phenotypic and Physiological Characterization Methods
Publication date: 2011 Source:Methods in Microbiology, Volume 38 Author(s): Noel R. Krieg , Penelope J. Padgett This chapter provides various methods that are useful for the physiological characterization of new taxa, as well the pertinent media and reagents involved. The chapter begins with fundamental characterization tests such as those for determining oxygen, carbon dioxide and hydrogen requirements; optimal temperature, salinity and pH and sole carbon and nitrogen sources. The chapter proceeds with methods to detect the ability to ferment or oxidize carbohydrates, end products of carbohydrate catabolism, nitrate...
Source: Methods in Microbiology - October 12, 2014 Category: Microbiology Source Type: research
2 How to Describe New Species of Prokaryotes
Publication date: 2011 Source:Methods in Microbiology, Volume 38 Author(s): Fred A. Rainey This chapter outlines the steps in the process of characterizing a bacterial or archaeal isolate or group of strains and presenting that information in the form of a taxonomic description. Prokaryotes are currently characterized using a polyphasic approach that brings together a variety of phenotypic, chemotaxonomic and genotypic data that comprise the formal description of a novel taxon. The first step in any characterization process is to determine the phylogenetic relationship to the type strains of previously described speci...
Source: Methods in Microbiology - October 12, 2014 Category: Microbiology Source Type: research
1 Taxonomy of Prokaryotes – Introduction
Publication date: 2011 Source:Methods in Microbiology, Volume 38 Author(s): Fred A. Rainey , Aharon Oren Prokaryote diversity has been the subject of increased attention in the past two decades. The most accepted concept, considered to be pragmatic and useful for species definition, is the so-called phylo-phenetic species concept—a monophyletic and genomically coherent cluster of individual organisms (strains) that show a high degree of overall similarity in many independent characteristics—and is diagnosable by one or more discriminative phenotypic properties. The species concept is based on a polyphasic approac...
Source: Methods in Microbiology - October 12, 2014 Category: Microbiology Source Type: research
Recent titles in the series
Publication date: 2011 Source:Methods in Microbiology, Volume 38 (Source: Methods in Microbiology)
Source: Methods in Microbiology - October 12, 2014 Category: Microbiology Source Type: research
Methods in Microbiology
Publication date: 2011 Source:Methods in Microbiology, Volume 38 (Source: Methods in Microbiology)
Source: Methods in Microbiology - October 12, 2014 Category: Microbiology Source Type: research
Chapter 6 Array-based approaches to bacterial transcriptome analysis
Publication date: 2012 Source:Methods in Microbiology, Volume 39 Author(s): Ulrike Mäder , Pierre Nicolas Microarray technology has been extensively used to compare or quantify genome-wide mRNA levels, a key factor in the adaptive response of bacteria to the environment. Classical gene expression arrays based on an existing genome annotation with relatively few probes for each gene, are well suited to assess the expression levels of all annotated transcripts under many different conditions. Newer genomic tiling arrays that cover both strands of a genome by overlapping probes and, more recently, RNA-seq approaches ha...
Source: Methods in Microbiology - October 12, 2014 Category: Microbiology Source Type: research
Chapter 5 Targeted and quantitative metabolomics in bacteria
Publication date: 2012 Source:Methods in Microbiology, Volume 39 Author(s): Hannes Link , Joerg Martin Buescher , Uwe Sauer Targeted metabolomics aims at reliable and sensitive quantification of a subset of metabolites in a cell. Here, we describe our current methods to obtain quantitative intracellular concentrations of a specified set of metabolites in bacteria. The protocol is structured into four steps of the workflow: standardized cultivation, sampling for metabolome analysis, extraction of metabolites and subsequent analysis by mass spectrometry. At the end, we give a brief discussion about the use of metaboli...
Source: Methods in Microbiology - October 12, 2014 Category: Microbiology Source Type: research
Chapter 4 Imaging fluorescent protein fusions in live bacteria
Publication date: 2012 Source:Methods in Microbiology, Volume 39 Author(s): Geoff Doherty , Karla Mettrick , Ian Grainge , Peter J. Lewis The use of fluorescent protein fusions has revolutionised our understanding of bacterial cell structure. Here we present a brief overview of the molecular toolkits available for the production of functional fluorescent protein fusions in Gram positive and Gram negative organisms. We highlight considerations for performing live cell imaging including equipment requirements and simple approaches to image processing. (Source: Methods in Microbiology)
Source: Methods in Microbiology - October 12, 2014 Category: Microbiology Source Type: research
Chapter 3 Proteomics From relative to absolute quantification for systems biology approaches
Publication date: 2012 Source:Methods in Microbiology, Volume 39 Author(s): Andreas Otto , Jörg Bernhardt , Michael Hecker , Uwe Völker , Dörte Becher Within the concert of OMICs technologies proteomics is particularly important for systems biology approaches because it provides large-scale, quantitative information on the effectors of cellular processes inside living organisms. For a comprehensive analysis of the proteome 2D-gel- based and gel-free, mass spectrometry-driven methods are available relying on different workflows for identification of proteins and time-resolved analysis of changes in their abundan...
Source: Methods in Microbiology - October 12, 2014 Category: Microbiology Source Type: research
