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Full Description
"Microbial Ecology: Culture-dependent Methods" is a comprehensive guide to studying microbial diversity. The book details methods for sampling and characterizing microbes from soil and water, covering both physicochemical and microbiological aspects. It delves into the cultivation, isolation, and preservation of bacteria and archaea, including cryopreservation and freeze-drying. Subsequent chapters focus on molecular techniques like DNA extraction, PCR, 16S rRNA gene sequencing, and bioinformatic analysis, along with advanced methods such as MLST, qPCR, and Whole Genome Sequencing. The book also covers sequence deposition and provides protocols for DGGE, making it an invaluable resource for microbial ecologists.
Contents
Preface. Samples and Sampling Methods for the Study of Microbial Diversity from Soil and Water. Physicochemical Characterization of Soil and Water Samples. Microbiological Characterization of Soil and Water Samples. Cultivation, Isolation, and Pure Culture of Bacteria and Archaea. Short-term and Long-term Preservation of Microorganisms at Extremely Low Temperatures. Long-term Preservation of Microorganisms using Freeze-drying. Biochemical Characterization of Bacteria. Tests for Screening: Aminopeptidase, KOH Test, and Antimicrobial Resistance. Bacterial DNA Extraction. A Detailed Method of Bacterial DNA Extraction using Sonication. DNA Quantification and Agarose Gel Electrophoresis. Amplification of the 16S rRNA using Polymerase Chain Reaction (PCR). PEG-NaCl Purification of PCR Products: Principles, Protocols, and Applications. 16S rRNA Gene Sequencing Method and Bioinformatic Analysis. Software Tools for Sequence Analysis and Identification. Deposition of Sequence Data in INSDC, ENA, and DDBJ Repositories. Deposition of Pure Cultures in International Culture Collections. Primer Design for Polymerase Chain Reactions (PCRs) and Sequencing PCRs. Loop-Mediated Isothermal Amplification (LAMP) Assay for Rapid Microbial Gene Detection. Multilocus Sequence Typing (MLST) for Microbial Identification and Classification. Quantitative Polymerase Chain Reaction (qPCR) Protocol and Applications. Whole Genome Sequencing (WGS) of Bacteria. Bacterial and Archaeal Genome Annotation. Denaturing Gradient Gel Electrophoresis (DGGE) Protocol and its Applications in Microbial Ecology. Index.
