New edition of the standard manual on molecular microbial ecology. Also available from Springer as an online version.
From the publisher's announcement:
Microbes are key drivers of the world's ecosystems. The vast majority of the world's diversity and metabolic potential lies within micro-organisms, yet we are just beginning to understand and utilize this ultimate resource of biological diversity. Critical to our exploration of the microbial world are methods that allow for the analysis of organisms that are invisible to our eyes, difficult to distinguish from each other, and often impossible to grow using available culture methods.
The field of microbial ecology has been revolutionized in the past two decades by the introduction of molecular methods into the toolbox of the microbial ecologist. This molecular arsenal has helped to unveil the enormity of microbial diversity across the breadth of the earth's ecosystems, and has revealed that we are only familiar with a very small minority of the organisms that carry out key microbial functions in diverse habitats. The Molecular Microbial Ecology Manual, Second Edition (MMEM-II) provides a detailed and user-friendly description of the methods that have made this revolution in microbial ecology possible. However, what is perhaps most exciting about MMEM-II is that it contains a large number of new chapters, highlighting the newest trends in microbial ecology research, which seek to provide more quantitative and statistically robust data, and means of coupling microbial identity and function. In addition, the majority of the proven methods described in MMEM's first version have undergone significant revisions to provide the most up-to-date applications available. The state-of-the-art methods described in MMEM-II have not only been provided by experts in the field, but in most cases by the laboratories that actually first developed and applied the methods, thus providing the MMEM-II user with unique first-hand tips and insight. The new on-line format available for MMEM-II should also add to the utility of MMEM-II by allowing users to search for key topics throughout the manual, skip between interrelated chapters at the push of a button, and by providing immediate availability to protocol updates and new chapters dedicated to future technical developments.
Supplement 1: 1.1.1. Extraction of microbial DNA from aquatic sources: Marine environments; J.H. Paul. 1.2.1. Extraction of microbial RNA from aquatic sources: Marine environments; S.L. Pichard, J.H. Paul. 1.3.2. Direct extraction of microbial DNA from soils and sediments; W.H. Johnston, et al. 1.4.1. Detection of microbial genes from the rhizosphere by magnetic capture hybridization and subsequent amplification of target genes by PCR; C. Jacobson. 2.1.1. Quantification of nucleic acids; V. Torsvik. 2.1.2. Parameters of nucleic acid hybridization experiments; C.N. Nakatsu, L.J. Forney. 2.8.2. Soil; E. Baath. - Basic Work: Extraction of Microbial DNA from Sewage and Manure; K. Smalla. Cell Extraction Method; V. Torsvik. Polymerase Chain Reaction (pcr) Analysis of Soil Microbial DNA; J.D. van Elsas, A.C. Wolters. Extraction and pcr Amplification of DNA from the Rhizoplane; P.A. Bramwell, et al. Extraction of Microbial DNA from the Phylloplane; P.A. Bramwell, et al. Extraction of Ribosomal DNA from Microbial Cultures; E. Stackebrandt, N. Ward. In situ Identification of Micro-organisms by Whole Cell Hybridization with RNA-Targeted Nucleic Acid Probes; R.I. Amann. Immunofluorescence Colony-Staining (IFC); J.W.L. van Vuurde, J.M. van der Wolf. Fluorescent Staining of Microbes for Total Direct Counts; J. Bloem. Natural Transformation in Aquatic Environments; J.H. Paul, H.G. Williams. Phage Ecology and Genetic Exchange in Soil; P.R. Herron. Design of Microcosms to Provide Data Reflecting Field Trials of GEMs; M.A. Hood, R. J. Seidler. Methods for Extracting DNA from Microbial Mats and Cultivated Micro-organisms: High Molecular Weight DNA from French Press Lysis; M.M. Bateson, D.M. Ward. Bacterial Community Fingerprinting of Amplified 16S and 16-23S Ribosomal DNA Gene Sequences and Restriction Endonuclease Analysis (ARDRA); A.A. Massol-Deya, et al. Detection of Gene Transfer in the Environment: Conjugation in Soil; E. Smit, J.D. van Elsas. Direct and Simultaneous Extraction of DNA and RNA from Soil; S. Selenska-Pobell. Sequence Databases; W. Ludwig. Extraction of Microbial Community DNA from Soils; J.D. van Elsas, K. Malla. Investigation of Fungal Phylogeny on the Basis of Small Ribosomal Subunit RNA Sequences; Y. van de Peer, R. de Wachter. Biodegradation Genes as Marker Genes in Microbial Ecosystems; B.M. Applegate, et al. Preparation of Radioactive Probes; M. Cunningham. Detection of Nucleic Acids by Chemiluminescence; M. Cunningham, et al. Gel Purification of Soil DNA Extracts; D.D. Myrold, et al. Detection of Microbial DNA Sequences by Colony Hybridization; P.R. Hirsch. Partial and Complete 16s RDNA Sequences, their Use in Generation of 16s RDNA Phylogenetic Trees and their Implications in Molecular Ecological Studies; E. Stackebrandt, F.A. Rainey. Extraction of Microbial DNA from Aquatic Sources: Freshwater; R.W. Pickup, et al. Slide Immunoenzymatic Assay (SIA); E.C. de Macario, A.J.L. Macario. (Part contents).