Environmental Microbiology: Methods and Protocols

ISBN-13: 9781617373701 / Angielski / Miękka / 2010 / 426 str.

John F. T. Spencer;Alicia L. Ragout De Spencer

Opis

The methods included in Environmental Microbiology: Methods and Pro- cols can be placed in the categories Communities and Biofilms, Fermented Milks, Recovery and Determination of Nucleic Acids, and the review s- tion, containing chapters on the endophytic bacterium, Bacillus mojavensis, the engineering of bacteria to enhance their ability to carry out bioremediation of aromatic compounds, using the hemoglobin gene from a strain of Vitreoscilla 23 spp., and the use of chemical shift reagents and Na NMR to study sodium gradients in microorganisms, all of which should be of interest to investigators in these fields. The subjects treated within the different categories also cover a wide range, with methods ranging from those for the study of marine organisms, through those for the investigation of microorganisms occurring in ground waters, including subsurface ground waters, to other types of environmental waters, to as varied subjects as the biodiversity of yeasts found in northwest Argentina. The range of topics described in the Fermented Milks section is smaller, but significant for investigators in areas concerned with milk as an item of foods for infants, small children, and even adults."

Spis treści

Part I. Communities and Biofilms Isolation and Molecular Characterization of Seawater Bacteria Juliana M. Benito, Gustavo A. Lovrich, Faustino Siñeriz, and Carlos M. Abate Reverse Sample Genome Probing to Monitor Microbial Communities E. Anne Greene and Gerrit Voordouw T-RFLP Analysis: A Rapid Fingerprinting Method for Studying Diversity, Structure, and Dynamics of Microbial Communities Werner Liesack and Peter F. Dunfield Assessing Bacterial DNA Content in Aquatic Systems Garrett W. Perney, Betsy R. Robertson, and D. K. Button Multiplexed Identification and Quantification of Analyte DNAs in Environmental Samples Using Microspheres and Flow Cytometry Mary Lowe, Alex Spiro, Anne O. Summers, and Joy Wireman Molecular Characterization of Microbial Communities From Marine Environments Nicolás G. Barengo, Juliana M. Benito, and Carlos M. Abate Yeasts: Ecology in Northwest Argentina Lucía I. C. de Figueroa, M. Alejandra Martínez, and John F. T. Spencer Aeromonads in Environmental Waters Anavella Gaitan Herrera Development of a Vital Fluorescent Staining Method for Monitoring Bacterial Transport in Subsurface Ground Water Mark E. Fuller Bench Scale Flow Cell for Nondestructive Imaging of Biofilms Eric S. Gilbert and Jay D. Keasling Part II. Fermented Milks a-Galactosidase Assay in Fermented Soymilk Products Marisa S. Garro, Graciela Font de Valdez, and Graciela Savoy de Giori Considerations to Avoid the Overestimation of Exopolysaccharides Produced by Lactic Acid Bacteria María Inés Torino and Graciela Font de Valdez Determination of Oligosaccharides in Fermented Soymilk Products by High-Performance Liquid Chromatography Marisa S. Garro, Graciela Font de Valdez, and Graciela Savoy de Giori Evaluation of Minimal Nutritional Requirements ofLactic Acid Bacteria Used in Functional Foods Elvira M. Hébert, Raúl R. Raya, and Graciela Savoy de Giori Part III. Nucleic Acids, Recovery, and Determination A Simple Method for Obtaining DNA Suitable for RAPD Analysis From Azospirillum Raúl O. Pedraza and Juan C. Díaz Ricci PCR Fingerprinting of rRNA Intergenic Spacer Regions for Molecular Characterization of Environmental Bacteria Isolates M. Alejandra Martínez and Faustino Siñeriz A DNA-DNA Hybridization Method for the Detection and Quantification of Specific Bacterial Taxa in Natural Environments Christopher E. Bagwell and Charles R. Lovell 13C and 1H NMR Study of the Glycogen Futile Cycle in Fibrobacter succinogenes Anne-Marie Delort, Genevieve Gaudet, and Evelyne Forano Chemical Analysis and Biological Removal of Wood Lipids Forming Pitch Deposits in Paper Pulp Manufacturing Ana Gutiérrez, José C. del Río, and Ángel T. Martínez Propolis: Chemical Micro-Heterogeneity and Bioactivity José Domingos Fontana, Juliana Adelmann, Mauricio Passos, Marcelo Maraschin, Cristina A. de Lacerda, and Fernando Mauro Lanças Enzymatic Saccharification of Cellulosic Materials Luiz Pereira Ramos and José Domingos Fontana Molecular Identification of Microbial Populations in Petroleum-Contaminated Groundwater Kazuya Watanabe, Natsuko Hamamura, and Nobuo Kaku Identification of Copper-Resistant Microorganisms by PCR Virginia H. Albarracín, Juliana M. Benito, Manuel Siñeriz Louis, María J. Amoroso, and Carlos M. Abate Selection of Tolerant Heavy Metal Yeasts From Different Polluted Sites Liliana Villegas, María J. Amoroso, and Lucía I. C. de Figueroa Medium for Differential Enumeration of Lactobacillus casei and Lactobacillus acidophilus From Lyophilized Mixed Cultures Mónica M. Locascio, Rosalía Alesso, Vilma I. Morata, and

Blurb

Understanding the relationship between a microorganism and its environment is essential to the successful manipulation of industrial, biochemical, and medical processes. In Environmental Microbiology: Methods and Protocols, highly practiced experimentalists who often have perfected the methods they write about describe readily reproducible techniques for determining most of the important factors governing microorganisms and their habitats. Presented in step-by-step detail, these cutting-edge methods range from those for the study of marine organisms, to those for investigating microorganisms occurring in groundwater, to the biodiversity found in remote environments. The protocols for studying fermented milks are significant for investigators concerned with milk as an item of food for infants, small children, and even adults. Additional methods for the recovery and determination of nucleic acids and other compounds affecting, and affected by, microorganisms, are provided for certain enzymes produced by plant pathogens and for obtaining microbial species tolerant of such inhibitors as heavy metals. Review articles discuss the endophytic bacterium Bacillus mojavensis, the engineering of bacteria to enhance their ability to carry out bioremediation of aromatic compounds, and the use of chemical shift reagents and Na-NMR to study sodium gradients in microorganisms. The protocols follow the successful Methods in Molecular Biology™ series format, each one offering step-by-step laboratory instructions, an introduction outlining the principle behind the technique, lists of equipment and reagents, and tips on troubleshooting and avoiding known pitfalls.
State-of-the-art and highly practical, Environmental Microbiology: Methods and Protocols offers microbiological researchers a powerful set of techniques for investigating and understanding microorganisms in their native environments.