Handbook of Methods in Aquatic Microbial Ecology is the first comprehensive compilation of 85 fundamental methods in modern aquatic microbial ecology. Each method is presented in a detailed, step-by-step format that allows readers to adopt new methods with little difficulty. The methods represent the state of the art, and many have become standard procedures in microbial research and environmental assessment. The book also presents practical advice on how to apply the methods. It will be an indispensable reference for marine and freshwater research laboratories, environmental assessment laboratories, and industrial research labs concerned with microbial measurements in water.
Table of Contents
Introduction (J.E. Hobbie). Isolation of Living Cells: Isolation and Enumeration of Anaerobic and Microaerophilic Bacteria in Aquatic Habitats (M.J. Ferrara-Guerrero, D.G. Marty, and A. Bianchi). Isolation and Culture of Hyperthermophilic Bacteria from Marine and Freshwater Habitats (J.A. Baross). Isolation of Psychrophilic Bacteria (R.Y. Morita). Isolation and Characterization of Bacteriocytes from a Bivalve-Sulfur Bacterium Symbiosis (S.C. Hand and A.E. Anderson). General Techniques for the Isolation and Culture of Marine Protists from Estuarine, Littoral, Psammolittoral, and Sublittoral Waters (J.J. Lee). Long-Term Culture of Marine Benthic Protists (P.G. Carey). Behavior and Bioenergetics of Anaerobic and Microaerobic Protists (B.J. Finlay). Culturing Free-Living Marine Phagotrophic Dinoflagellates (E.J. Lessard). Enrichment, Isolation, and Culture of Free-Living Heterotrophic Flagellates (D.A. Caron). Determination of Pressure Effects on Flagellates Isolated from Surface Waters (C.M. Turley). Isolation, Cloning, and Axenic Culturing of Marine Ciliates (A.T. Soldo and S.A. Brickson). Isolation and Laboratory Culture of Marine Oligotrichous Ciliates (D.J. Gifford). Extraction of Protists in Aquatic Sediments via Density Gradient Cetrifugation (D.M. Alongi). Identification, Enumeration, and Diversity: Statistical Analysis of Direct Counts of Microbial Abundance (D.L. Kirchman). Enumeration and Isolation of Viruses (C.A. Suttle). Total Count of Viruses in Aquatic Environments (G. Bratbak and M. Heldal). Improved Sample Preparation for Enumeration of Aggregated Aquatic Substrate Bacteria (M.I. Velji and L.J. Albright). Direct Estimates of Bacterial Numbers in Seawater Samples without Incurring Cell Loss Due to Sample Storage (C.M. Turley). Total and Specific Bacterial Counts by Simultaneous Staining with DAPI and Fluorochrome-Labeled Antibodies (K.A. Hoff). Use of RFLPs for the Comparison of Marine Cyanobacteria (S.E. Douglas). Use of High-Resolution Flow Cytometry to Determine the Activity and Distribution of Aquatic Bacteria (D.K. Button and B.R. Robertson). Phytoplankton Analysis Using Flow Cytometry (R.J. Olson, E.R. Zettler, and M.D. DuRand). Enumeration of Phototrophic Picoplankton by Autofluorescence Microscopy (E.A. MacIsaac and J.G. Stockner). Estimating Cell Concentration and Biomass of Autotrophic Plankton Using Microscopy (B.C. Booth). Preservation and Storage of Samples for Enumeration of Heterotrophic Protists (E.B. Sherr and B.F. Sherr). Staining of Heterotrophic Protists for Visualization via Epifluorescence Microscopy (E.B. Sherr, D.A. Caron, and B.F. Sherr). A Quantitative Protargol Stain (QPS) for Ciliates and Other Protists (D.J.S. Montagnes and D.H. Lynn). Preparation of Pelagic Protists for Electron Microscopy (B.S.C. Leadbeater). A Rapid Technique for the Taxonomy of Methanogenic Bacteria: Comparison of the Methylreductase Subunits (P.E. Rouviére and C.H. Kuhner). Extraction of DNA from Soils and Sediments (R.M. Atlas). Detecting Gene Sequences Using the Polymerase Chain Reaction (R.M. Atlas). Quantitative Description of Microbial Communities Using Lipid Analysis (R.H. Findlay and F.C. Dobbs). Single Cell Identification Using Fluorescently Labeled, Ribosomal RNA-Specific Probes (E.F. DeLong). Immunofluorescence Method for the Detection and Characterization of Marine Microbes (L. Campbell). Biomass: The Relationship between Biomass and Volume of Bacteria (S. Norland). Microscope Methods for Measuring Bacterial Biovolume: Epifluorescence Microscopy, Scanning Electron Microscopy, and Transmission Electron Microscopy (G. Bratbak). Measurement of Carbon and Nitrogen Biomass and Biovolume from Naturally Derived Marine Bacterioplankton (S. Lee). Use of Color Image Analysis and Epifluorescence Microscopy to Measure Plankton Biomass (P.G. Verity and M.E. Sieracki). Determination of Size and Morphology of Aquatic Bacteria by Automated Image Analysis (R. Psenner). Analysis of Microbial Lipids to Determine Biomass and Detect the Response of Sedimentary Microorganisms to Disturbance (F.C. Dobbs and R.H. Findlay). Total Microbial Biomass Estimation Derived from the Measurement of Particulate Adenosine-5'-Triphosphate (D.M. Karl). Microphytobenthic Biomass Measurement Using HPLC and Conventional Pigment Analysis (C. Riaux-Gobin and B. Klein). Microphotometric Analysis of the Spectral Absorption and Fluorescence of Individual Phytoplankton Cells and Detrital Matter (R. Iturriaga and S.L. Bower). Measurement of Elemental Content and Dry Weight of Single Cells: X-Ray Microanalysis (M. Heldal). Activity, Respiration, and Growth: Microautoradiographic Detection of Microbial Activity (K.R. Carman). 14C Tracer Method for Measuring Microbial Activity in Deep-Sea Sediments (J.W. Deming). Evaluating Bacterial Activity from Cell-Specific Ribosomal RNA Content Measured with Oligonucleotide Probes (P.F. Kemp, S. Lee, and J. LaRoche). Use of Fluorogenic Model Substrates for Extracellular Enzyme Activity (EEA) Measurement of Bacteria (H.-G. Hoppe). Photoassimilation of Acetate by Algae (R.L. Cuhel). Starvation-Survival Strategies in Bacteria (R.Y. Morita). Community Respiration Measurements Using a Pulsed O2 Electrode (C. Langdon). Sediment Community Production and Respiration Measurements: The Use of Microelectrodes and Bell Jars (P.A.G. Hofman and S.A. de Jong). Distinguishing Bacterial from Nonbacterial Decomposition of Spartina alterniflora by Respirometry (D.E. Padgett). Microbial RNA and DNA Synthesis Derived from the Assimilation of [2,3H]-Adenine (D.M. Karl). Adenosine Triphosphate (ATP) and Total Adenine Nucleotide (TAN) Pool Turnover Rates as Measures of Energy Flux and Specific Growth Rate in Natural Populations of Microorganisms (D.M. Karl). Estimating Production of Heterotrophic Bacterioplankton via Incorporation of Tritiated Thymidine (R.I. Bell). Thymidine Incorporation into DNA as an Estimate of Sediment Bacterial Production (S. Findlay). Leucine Incorporation as a Measure of Biomass Production by Heterotrophic Bacteria (D. Kirchman). Estimating Conversion Factors for the Thymidine and Leucine Methods for Measuring Bacterial Production (D.L. Kirchman and H.W. Ducklow). Bacterial Production in Anaerobic Water Columns (C. Pedrós-Alió, J.G. Cantizano, and J.I. Calderón). Production of Heterotrophic Bacteria Inhabiting Marine Snow (A. Alldredge). Bacterial Growth Rates Measured by Pulse Labeling (P. La Rock and J.-H. Hyun). Utilization of Amino Acids and Precursors for Amino Acid De Novo Synthesis by Planktonic Bacteria (M. Simon). Dialysis Bag Incubation as a Nonradiolabeling Technique to Estimate Bacterioplankton Production In Situ (G.J. Herndl, E. Kaltenböck, and G. Müller-Niklas). Growth Rates of Natural Populations of Heterotrophic Nanoplankton (G.B. McManus). The Labeled Chlorophyll a Technique for Determining Photoautotrophic Carbon-Specific Growth Rates and Carbon Biomass (D.G. Redalje). Incorporation of 14CO2 into Protein as an Estimate of Phytoplankton N-Assimilation and Relative Growth Rate (G.R. DiTullio). Membrane-Containing Fungal Mass and Fungal Specific Growth Rate in Natural Samples (S.Y. Newell). Organic Matter Decomposition and Nutrient Regeneration: Radiotracer Approaches for the Study of Plant Polymer Biodegradation (R. Benner). Estimating Degradation Rates of Chitin in Aquatic Samples (M.T. Montgomery and D.L. Kirchman). Measurement of Dimethylsulfide (DMS) and Dimethylsulfoniopropionate (DMSP) in Seawater and Estimation of DMA Turnover Rates (R.P. Kiene). Sulfate Assimilation by Aquatic Microorganisms (R.L. Cuhel). Determination of Nitrogenase Activity in Aquatic Samples Using the Acetylene Reduction Procedure (D.G. Capone). Denitrification and Nitrification Rates in Aquatic Sediments (S.P. Seitzinger). Turnover of 15NH4+ Tracer in Sediments (T.H. Blackburn). Microbial Cycling of Inorganic and Organic Phosphorus in the Water Column (J.W. Ammerman). Food Webs and Trophic Interactions: Approaches for Measuring Stable Carbon and Nitrogen Isotopes in Bacteria (R.B. Coffin and L.A. Cifuentes). Bacterial Sinking Losses (C. Pedrós-Alió and J. Mas). Methods for the Observation and Use in Feeding Experiments of Microbial Exopolymers (A.W. Decho). Protistan Grazing Rates via Uptake of Fluorescently Labeled Prey (E.B. Sherr and B.F. Sherr). Grazing Rate of Bacterioplankton via Turnover of Genetically Marked Minicells (J. Wikner). Estimating Rates of Growth and Grazing Mortality of Phytoplankton by the Dilution Method (M.R. Landry). Consumption of Protozoa by Copepods Feeding on Natural Microplankton Assemblages (D.J. Gifford). Predation on Planktonic Protists Assessed by Immunochemical Assays (M.D. Ohman). Absorption of Microbes by Benthic Macrofauna by the 14C:51Cr Dual-Labeling Method (G. Lopez). Radioisotope Technique to Quantify In Situ Microbivory by Meiofauna in Sediments (P.A. Montagna). Index.