This book is a comprehensive guide to studying microbial diversity. It 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.
"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.
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.
Dr. Bhagwan (MSc, PhD, MCA) is an eminent researcher in Microbiome Diversity and Microbiome. After completing his postdoctoral fellowship at BRIC-NCCS (Pune), he joined Savitribai Phule Pune University, often called "the Oxford of the East," as an Assistant Professor. He is an Associate Professor at the Yenepoya Research Centre, Yenepoya (Deemed to be University) in Mangalore, India. His current specialization is Computational Biology and Evolutionary Microbiology.
He serves as the expert for the European Commission, the French Foundation for Medical Research (France), the National Research and Development Agency (Chile), Certified Educator and Ambassador for GPTZero (USA), and the Academic Advisor for Fengkai Group Co., Limited (Hong Kong) for various international and national agencies. Since 2022, he has consistently been ranked on the AD Scientific Index (five times, ID: 4509536). His research is featured by Nature and The Times of India.
