Handbook of Methods in Aquatic Microbial Ecology/ edited by Paul F. Kemp [ et al.]

Table of contents

Chapter 1|11 pages
Isolation and Enumeration of Anaerobic and Microaerophiiic Bacteria in Aquatic Habitats
ByM. J. Ferrara-Guerrero, D. G. Marty, A. Bianchi
Abstract

Chapter 2|10 pages
Isolation and Cultivation of Hyperthermophilic Bacteria from Marine and Freshwater Habitats
ByJohn A. Baross
Abstract

Chapter 3|2 pages
Isolation of Psychrophilic Bacteria
ByRichard Y. Morita
Abstract

Chapter 4|7 pages
Isolation and Characterization of Bacteriocytes from a Bivalve-Sulfur Bacterium Symbiosis
BySteven C. Hand, Amy E. Anderson
Abstract

Chapter 5|10 pages
General Techniques for the Isolation and Culture of Marine Protists from Estuarine, Littoral, Psammolittoral, and Sublittoral Waters
ByJohn J. Lee
Abstract

Chapter 6|8 pages
Long-Term Culture of Marine Benthic Protists
ByPhilip G. Carey
Abstract

Chapter 7|8 pages
Behavior and Bioenergetics of Anaerobic and Microaerobic Protists
ByB. J. Finlay
Abstract

Chapter 8|9 pages
Culturing Free-Living Marine Phagotrophic Dinoflagellates
ByEvelyn J. Lessard
Abstract

Chapter 9|13 pages
Enrichment, Isolation, and Culture of Free-Living Heterotrophic Flagellates
ByDavid A. Caron
Abstract

Chapter 10|6 pages
Determination of Pressure Effects on Flagellates Isolated from Surface Waters
ByC. M. Turley
Abstract

Chapter 11|5 pages
Isolation, Cloning, and Axenic Cultivation of Marine Cilliates
ByA. T. Soldo, S. A. Brickson
Abstract

Chapter 12|6 pages
Isolation and Laboratory Culture of Marine Oligotrichous Ciliates
ByDian J. Gifford
Abstract

Chapter 13|6 pages
Extraction of Protists in Aquatic Sediments via Density Gradient Centrifugation
ByDaniel M. Alongi
Abstract
Section II|186 pages
Identification, Enumeration, and Diversity

Chapter 14|3 pages
Statistical Analysis of Direct Counts of Microbial Abundance
ByDavid L. Kirchman
Abstract

Chapter 15|14 pages
Enumeration and Isolation of Viruses
ByCurtis A. Suttle
Abstract

Chapter 16|4 pages
Total Count of Viruses in Aquatic Environments
ByGynoar Bratbak, Mikal Heldal
Abstract

Chapter 17|4 pages
Improved Sample Preparation for Enumeration of Aggregated Aquatic Substrate Bacteria
ByM. Iqubal Velji, Lawrence J. Albright
Abstract

Chapter 18|5 pages
Direct Estimates of Bacterial Numbers in Seawater Samples Without Incurring Cell Loss Due to Sample Storage
ByC.M. Turley
Abstract

Chapter 19|6 pages
Total and Specific Bacterial Counts by Simultaneous Staining with DAPI and Fluorochrome-Labeled Antibodies
ByKjell Arne Hoff
Abstract

Chapter 20|7 pages
Use of RFLPs for the Comparison of Marine Cyanobacteria
BySusan E. Douglas
Abstract

Chapter 21|11 pages
Use of High-Resolution Flow Cytometry to Determine the Activity and Distribution of Aquatic Bacteria
ByD. K. Button, B. R. Robertson
Abstract

Chapter 22|12 pages
Phytoplankton Analysis Using Flow Cytometry
ByRobert J. Olson, Erik R. Zettler, Michele D. DuRand
Abstract

Chapter 23|11 pages
Enumeration of Phototrophic Picoplankton by Autofluorescence Microscopy
ByErland A. Maclsaac, John G. Stockner
Abstract

Chapter 24|7 pages
Estimating Cell Concentration and Biomass of Autotrophic Plankton Using Microscopy
ByBeatrice C. Booth
Abstract

Chapter 25|6 pages
Preservation and Storage of Samples for Enumeration of Heterotrophic Protists
ByEvelyn B. Sherr, Barry F. Sherr
Abstract

Chapter 26|15 pages
Staining of Heterotrophic Protists for Visualization via Epifluorescence Microscopy
ByEvelyn B. Sherr, David A. Caron, Barry F. Sherr
Abstract

Chapter 27|12 pages
A Quantitative Protargol Stain (QPS) for Ciliates and Other Protists
ByD. J. S. Montagnes, D. H. Lynn
Abstract

Chapter 28|11 pages
Preparation of Pelagic Protists for Electron Microscopy
ByB. S. C. Leadbeater
Abstract

Chapter 29|8 pages
A Rapid Technique for the Taxonomy of Methanogenic Bacteria: Comparison of the Methylreductase Subunits
ByPierre E. Bouvière, Carla H. Kuhner
Abstract

Chapter 30|6 pages
Extraction of DNA from Soils and Sediments
ByRonald M. Atlas
Abstract

Chapter 31|4 pages
Detecting Gene Sequences Using the Polymerase Chain Reaction
ByRonald M. Atlas
Abstract

Chapter 32|14 pages
Quantitative Description of Microbial Communities Using Lipid Analysis
ByRobert H. Findlay, Fred C. Dobbs
Abstract

Chapter 33|10 pages
Single-Cell Identification Using Fluorescently Labeled, Ribosomal RNA-Specific Probes
ByEdward F. DeLong
Abstract

Chapter 34|6 pages
Immunofluorescence Method for the Detection and Characterization of Marine Microbes
ByLisa Campbell
Abstract
Section III|94 pages
Biomass

Chapter 35|5 pages
Section BiomassThe Relationship Between Biomass and Volume of Bacteria
BySvein Norland
Abstract

Chapter 36|9 pages
Microscope Methods for Measuring Bacterial Biovolume: Epifluorescence Microscopy, Scanning Electron Microscopy, and Transmission Electron Microscopy
ByGunnar Bratbak
Abstract

Chapter 37|7 pages
Measurement of Carbon and Nitrogen Biomass and Biovolume from Naturally Derived Marine Bacterioplankton
BySangHoon Lee
Abstract

Chapter 38|12 pages
Use of Color Image Analysis and Epifluorescence Microscopy to Measure Plankton Biomass
ByPeter G. Verity, Michael E. Sieracki
Abstract

Chapter 39|7 pages
Determination of Size and Morphology of Aquatic Bacteria by Automated Image Analysis
ByRoland Psenner
Abstract

Chapter 40|12 pages
Analysis of Microbial Lipids to Determine Biomass and Detect the Response of Sedimentary Microorganisms to Disturbance
ByFred C. Dobbs, Robert H. Findlay
Abstract

Chapter 41|10 pages
Total Microbial Biomass Estimation Derived from the Measurement of Particulate Adenosine-5‘-Triphosphate
ByDavid M. Karl
Abstract

Chapter 42|8 pages
Microphytobenthic Biomass Measurement Using HPLC and Conventional Pigment Analysis
ByCatherine Riaux-Gobin, Bert Klein
Abstract

Chapter 43|9 pages
Microphotometric Analysis of the Spectral Absorption and Fluorescence of Individual Phytoplankton Cells and Detrital Matter
ByRodolfo Iturriaga, Susan L. Bower
Abstract

Chapter 44|8 pages
Measurement of Elemental Content and Dry Weight of Single Cells: X-Ray Microanalysis
ByMikal Heldal
Abstract
Section IV|192 pages
Activity, Respiration, and Growth

Chapter 45|8 pages
Microautoradiographic Detection of Microbial Activity
ByKevin R. Carman
Abstract

Chapter 46|10 pages
14C Tracer Method for Measuring Microbial Activity in Deep-Sea Sediments
ByJody W. Deming
Abstract

Chapter 47|8 pages
Evaluating Bacterial Activity from Cell-Specific Ribosomal RNA Content Measured with Oligonucleotide Probes
ByP. F. Kemp, S. Lee, J. LaRoche
Abstract

Chapter 48|9 pages
Use of Fluorogenic Model Substrates for Extracellular Enzyme Activity (EEA) Measurement of Bacteria
ByHans-Georg Hoppe
Abstract

Chapter 49|8 pages
Photoassimilation of Acetate by Algae
ByRussell L. Cuhel
Abstract

Chapter 50|5 pages
Starvation-Survival Strategies in Bacteria
ByRichard Y. Morlta
Abstract

Chapter 51|7 pages
Community Respiration IVIeasurements Using a Pulsed O 2 Electrode
ByChristopher Langdon
Abstract

Chapter 52|9 pages
Sediment Community Production and Respiration Measurements: The Use of Microelectrodes and Bell Jars
ByP. A. G. Holman, S. A. de Jong
Abstract

Chapter 53|5 pages
Distinguishing Bacterial from Nonbacterial Decomposition of Spartina alterniflora by Respirometry
ByDavid E. Padgett
Abstract

Chapter 54|11 pages
Microbial RNA and DNA Synthesis Derived from the Assimilation of [2, 3H]-Adenine
ByDavid M. Karl
Abstract

Chapter 55|12 pages
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
ByDavid M. Karl
Abstract

Chapter 56|9 pages
Estimating Production of Heterotrophic Bacterioplankton via Incorporation of Tritiated Thymidine
ByRussell T. Bell
Abstract

Chapter 57|3 pages
Thymidine Incorporation into DNA as an Estimate of Sediment Bacterial Production
ByStuart Findlay
Abstract

Chapter 58|4 pages
Leucine Incorporation as a Measure of Biomass Production by Heterotrophic Bacteria
ByDavid L. Kirchman
Abstract

Chapter 59|5 pages
Estimating Conversion Factors for the Thymidine and Leucine Methods for Measuring Bacterial Production
ByDavid L. Kirchman, Hugh W. Ducklow
Abstract

Chapter 60|12 pages
Bacterial Production in Anaerobic Water Columns
ByCarlos Pedrós-Alió, Josefina García-Cantizano, Juan I. Calderón
Abstract

Chapter 61|6 pages
Production of Heterotrophic Bacteria Inhabiting Marine Snow
ByAlice L. Alldredge
Abstract

Chapter 62|10 pages
Bacterial Growth Rates Measured by Pulse Labeling
ByPaul La Rock, Jung-Ho Hyun
Abstract

Chapter 63|6 pages
Utilization of Amino Acids and Precursors for Amino Acid De Novo Synthesis by Planktonic Bacteria
ByMeinhard Simon
Abstract

Chapter 64|4 pages
Dialysis Bag Incubation as a Nonradiolabeling Technique to Estimate Bacterioplankton Production In Situ
ByGerhard J. Herndl, Elisabeth Kaltenböck, Gerald Müller-Niklas
Abstract

Chapter 65|6 pages
Growth Rates of Natural Populations of Heterotrophic Nanoplankton
ByGeorge B. McManus
Abstract

Chapter 66|10 pages
The Labeled Chlorophyll a Technique for Determining Photoautotrophic Carbon Specific Growth Rates and Carbon Biomass
ByDonald G. Redalje
Abstract

Chapter 67|6 pages
Incorporation of 14CO2 into Protein as an Estimate of Phytoplankton N-Assimilation and Relative Growth Rate
ByGiacomo R. DiTullio
Abstract

Chapter 68|8 pages
Membrane-Containing Fungal Mass and Fungal Specific Growth Rate in Natural Samples
BySteven Y. Newell
Abstract
Section V|74 pages
Organic Matter Decomposition and Nutrient Regeneration

Chapter 69|7 pages
Radiotracer Approaches for the Study of Plant Polymer Biodegradation
ByRonald Benner
Abstract

Chapter 70|4 pages
Estimating Degradation Rates of Chitin inAquatic Samples
ByMichael T. Montgomery, David L. Kirchman
Abstract

Chapter 71|10 pages
Measurement of Dimethylsulfide (DMS) and Dimethylsulfoniopropionate (DMSP) in Seawater and Estimation of DMS Turnover Rates
ByRonald P. Kiene
Abstract

Chapter 72|9 pages
Sulfate Assimilation by Aquatic Microorganisms
ByRussell L. Cuhel
Abstract

Chapter 73|11 pages
Determination of Nitrogenase Activity in Aquatic Samples Using the Acetylene Reduction Procedure
ByDouglas G. Capone
Abstract

Chapter 74|9 pages
Denitrification and Nitrification Rates in Aquatic Sediments
BySybil P. Seitzinger
Abstract

Chapter 75|6 pages
Turnover of 15NH4 + Tracer in Sediments
ByT. H. Blackburn
Abstract

Chapter 76|12 pages
Microbial Cycling of Inorganic and Organic Phosphorus in the Water Column
ByJames W. Ammerman
Abstract
Section VI|93 pages
Food Webs and Trophic Interactions

Chapter 77|13 pages
Approaches for Measuring Stable Carbon and Nitrogen Isotopes in Bacteria
ByRichard B. Coffin, Luis A. Cifuentes
Abstract

Chapter 78|8 pages
Bacterial Sinking Losses
ByCarlos Pedrós-Alió, Jordi Mas
Abstract

Chapter 79|10 pages
Methods for the Observation and Use in Feeding Experiments of Microbial Exopolymers
ByAlan W. Decho
Abstract

Chapter 80|7 pages
Protistan Grazing Rates via Uptake of Fluorescently Labeied Prey
ByEvelyn B. Sherr, Barry F. Sherr
Abstract

Chapter 81|12 pages
Grazing Rate of Bacterioplankton via Turnover of Genetically Marked Minicells
ByJohao Wikner
Abstract

Chapter 82|8 pages
Estimating Rates of Growth and Grazing Mortality of Phytoplanlcton by the Dilution Method
ByMichael R. Landry
Abstract

Chapter 83|7 pages
Consumption of Protozoa by Copepods Feeding on Natural Microplankton Assemblages
ByDian J. Gifford
Abstract

Chapter 84|7 pages
Predation on Planktonic Protists Assessed by Immunochemical Assays
ByMark D. Ohman
Abstract

Chapter 85|6 pages
Absorption of Microbes by Benthic Macrofauna by the 14C:51Cr Dual-Labeling Method
ByGlenn Lopez
Abstract

Chapter 86|9 pages
Radioisotope Technique to Quantify In Situ Microbivory by Meiofauna in Sediments
ByPaul A. Montagna
Abstract

Includes bibliographical references and index.

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