Molecular Microbial Ecology Manual

For a long time microbial ecology has been developed as a distinct field with­ in Ecology. In spite of the important role of microorganisms in the environ­ ment, this group of 'invisible' organisms remained unaccessable to other ecologists. Detection and identification of microorganisms remain largely dependent on isolation techniques and characterisation of pure cultures. We now realise that only a minor fraction of the microbial community can be cultivated. As a result of the introduction of molecular methods, microbes can now be detected and identified at the DNA/RNA level in their natural environment. This has opened a new field in ecology: Molecular Microbial Ecology. In the present manual we aim to introduce the microbial ecologist to a selected number of current molecular techniques that are relevant in micro­ bial ecology. The first edition of the manual contains 33 chapters and an equal number of additional chapters will be added this year. Since the field of molecular ecology is in a continuous progress, we aim to update and extend the Manual regularly and will invite anyone to deposit their new protocols in full detail in the next edition of this Manual.

Preface. Section 1: Isolation of Microbial Nucleic Acids. 1.1: Extraction of Microbial DNA from Aquatic Sources. 1.2: Extraction of Microbial RNA from Aquatic Sources. 1.3: Extraction of Microbial RNA from Bulk Soil. 1.4: Extraction of DNA from Phytosphere, Rhizosphere, Rhizoplane. 1.5: Extraction of RNA from Bulk Soil. 1.6: Nucleic Acid Extraction from Cultures. Section 2: Detection of Microbial Nucleic Acid Sequences. 2.2: Preparation of Radioactive Probes. 2.3: Preparation of Non-Radioactive Probes. 2.6: Detection of Microbial DNA Sequences by Colony Hybridization. 2.7: Detection and Quantification of Microbial Nucleic Acid Sequence Polymerase Chain Reaction (PCR). Section 3: Identification and Classification of Microbes Using DNA and RNA Sequences. 3.1: Partial and Complete 16S rDNA Sequences, Their Use in Generation of 16S rDNA Phylogenetic Trees and Their Implications in Molecular Ecological Studies. 3.3: Microbial identification and Design of Phylogenetic Trees Based on rRNA Sequences. Section 4: Detection, Identification and Classification of Microbes Using Other Methods. 4.1: Detection, Identification and Classification of Microbes Using Other Methods. Section 5: Detection of Gene Transfer in the Environment. 5.1: Gene Transfer by Transformation. 5.2: Gene Transfer by Conjugation. 5.3: Gene Transfer by Transduction. Section 6: Tracking of Specific Microbes in the Environment. 6.1: Marker Genes. 6.2: Designing Field and Microcosm Experiments with GEM's. Index.