Techniques in Microbial Ecology

by Burlage, Robert S.; Atlas, Ronald; Stahl, David; Geesey, Gill; Sayler, Gary

• ISBN13: 9780195092233
• ISBN10: 0195092236
• Format: Spiral Bound
• Copyright: 1998-03-26
• Publisher: Oxford University Press

Summary

Microbial ecology is one of the fastest growing fields of microbiology. This practical volume is the bench and field scientist's guide to well-established techniques for investigating microbial communities. Both for biologists just entering the field and for experienced researchers wishingto explore new areas, this book provides the theoretical background, detailed protocols, and tips from experts for working in this field. Chapters on bacteria with interesting metabolic traits are augmented with chapters on molecular techniques, lipid analysis, and appropriate sampling techniques.The final section includes up-to-date information on biofilm development and study, the science and practice of bioremediation, modeling of biological systems (including the most useful statistical parameters), and the study of phylogenetics.

Table of Contents

Contributors	xi
PART I ENVIRONMENTAL MICROBIOLOGY	3	(236)
1 Microbially Mediated Nitrogen Cycling	3	(28)
Hans W. Paerl
Biologically Available Forms of Nitrogen: Analyses	5	(3)
Nitrogen Transformations: Characterizing Relevant Microbiota and their Activities	8	(19)
References	27	(4)
2 Microbes of the Sulfur Cycle	31	(27)
Don P. Kelly
Ann P. Wood
Techniques	32	(2)
Types of Bacteria	34	(1)
Stock Solutions and Culture Media	35	(8)
Assays of Substrates and Intermediates	43	(9)
Enzyme Assays	52	(4)
References	56	(2)
3 Isolation, Cultivation and Characterization of Iron- and Manganese-Reducing Bacteria	58	(21)
Joel Kostka
Kenneth H. Nealson
Media Preparation	60	(3)
Preparation of the Oxidized Metals	63	(5)
Monitoring Metal Reduction in Culture	68	(2)
Enrichment, Estimation of Abundance, and Isolation of Metal-Reducing Bacteria	70	(4)
Growth in the Laboratory: General Considerations	74	(1)
Conclusion	75	(1)
References	75	(4)
4 The Aerobic, Hydrogen-Oxidizing (Knallgas) Bacteria	79	(34)
Michel Aragno
Hydrogen in Natural Environments	87	(2)
Culture Methods	89	(10)
Identification	99	(7)
References	106	(7)
5 Methanogens	113	(24)
Stephen H. Zinder
Cultural Methods for Studying Methanogens	116	(8)
Methods to Quantify Methanogenic Activity	124	(3)
Microscopic Methods to Study Methanogens in Natural Habitats	127	(3)
References	130	(7)
6 Ecology of Methylotrophic Bacteria	137	(26)
Richard S. Hanson
Measurements of Methane Oxidation in Environmental Samples	141	(4)
Isolation of Pure Cultures of Methylotrophic Bacteria from Natural Samples and their Characterization	145	(6)
Detection of Methylotrophic Bacteria in Environmental Samples Using Gene Probes and Phylogenetic Probes	151	(4)
Ecologic Studies that Have Employed Gene and Phylogenetic Probes	155	(3)
Growth Media	158	(2)
References	160	(3)
7 Terrestral Fungal Communities	163	(40)
Alan D.M. Rayner
Lynne Boddy
Locating and Identifying Fungi	164	(8)
Isolation of Spores-Non-Species-Specific Techniques	172	(3)
Isolation of Culturable Fungi-From Mycelia	175	(1)
Molecular Detection of Unculturable Fungi	176	(1)
Identifying Cultures and Spores	177	(4)
Interpreting Distribution Patterns from an Organizational Viewpoint	181	(13)
Snapshots of Metabolic Activity	194	(4)
References	198	(5)
8 Rapid Techniques for the Identification of Free-Living Protozoa	203	(15)
G.F. Esteban
K.J. Clarke
B.J. Finlay
Identifying Ciliated Protozoa with the Silver Carbonate Impregnation Technique	204	(3)
Rapid Specimen Preparation Methods for Electron Microscopy	207	(9)
References	216	(2)
9 Methods for Enumeration and Characterization of Bacteriophages from Environmental Samples	218	(21)
Robert V. Miller
Laboratory Techniques	219	(6)
Genetic Methods: Transductional Analysis	225	(2)
Environmental Methods	227	(6)
References	233	(6)
PART II ENVIRONMENTAL TECHNIQUES	239	(98)
10 Sampling And Enumeration Techniques	239	(16)
J.K. Fredrickson
D.L. Balkwill
Methods for Sampling Environmental Media	240	(4)
Total Counting and Biomass Methods	244	(7)
Examples of Media for Plating Soil and Subsurface Sediment Samples	251	(1)
References	252	(3)
11 Signature Lipid Biomarker Analysis	255	(18)
David C. White
David B. Ringelberg
Lipid Extraction	255	(3)
Silicic Acid Column Chromatography	258	(1)
Preparation of Fatty Acid Methyl Esters from Esterified Lipids	259	(2)
Separation, Quantification, and Identification of Organic Compounds	261	(2)
Preparation of Poly-Beta-Hydroxyalkanoates from Glycolipids	263	(2)
Preparation of Sterols from Esterified Lipids	265	(1)
Preparation of Lipopolysaccharide Hydroxy Fatty Acids	266	(2)
Preparation of Dimethyl Disulfide Adducts of Monounsaturated Fame	268	(1)
Preparation of Archaebacterial or Thermodesulfobacterium commune Ether Lipids for Supercritical Fluid Chromatography	269	(2)
References	271	(2)
12 Isolation of Nucleic Acids From Environmental Samples	273	(16)
Andrew Ogram
Factors Affecting Recovery of Nucleic Acids	274	(6)
Cell Fractionation Versus Direct Lysis	280	(1)
Methods	281	(6)
References	287	(2)
13 Molecular Techniques	289	(48)
Robert S. Burlage
Gene Cloning-an Overview	290	(16)
DNA Transfer	306	(6)
Hybridization Analysis	312	(10)
Polymerase Chain Reaction	322	(6)
Restriction Fragment Length Polymorphism	328	(2)
DNA Sequencing	330	(1)
References	331	(6)
PART III SPECIAL TOPICS	337	(118)
14 Laboratory Studies of Bacterial Biofilms	337	(17)
M.W. Mittelman
Test Systems	338	(8)
Quantitative Recovery of Cells from Surfaces	346	(1)
Evaluation of Bacterial Numbers	347	(2)
Determination of Biofilm Biomass Constituents	349	(1)
Determination of Biofilm Metabolic Activity	350	(1)
Electron Microscopic Examination of Biofilm Architecture	351	(1)
References	352	(1)
Bibliography	352	(2)
15 Theoretical and Applied Aspects of Bioremediation: The Influence of Microbiological Processes on Organic Contaminant Compounds in Field Sites	354	(54)
Eugene L. Madsen
Conceptual Overview of Bioremediation	355	(8)
Techniques of Bioremediation and Biodegradation	363	(31)
Concluding Remarks	394	(1)
References	394	(14)
16 Mathematical Modeling and Statistical Analysis	408	(30)
J.I. Prosser
Mathematical Models	408	(11)
Statistical Analysis	419	(17)
Conclusions	436	(1)
References	436	(2)
17 Numerical Classification Methods	438	(17)
Estelle Russek-Cohen
Rita R. Colwell
Data Quality	439	(3)
Tree Construction	442	(6)
Evaluation and Validation of Results	448	(1)
Identification	449	(3)
Ordination Methods	452	(1)
References	452	(3)
Index	455