Manual of Environmental Microbiology

Introduction to environmental microbiology p. 3 Neighborhoods and community involvement : no microbe is an island p. 6 Prokaryotic diversity : form, ecophysiology, and habitat p. 20 Overview : general microbiology p. 37 Analytical imaging and microscopy techniques p. 40 Cultivation of bacteria and fungi p. 69 Cultivation of algae and protozoa p. 79 Cultivation and assay of animal viruses p. 93 Cultivation of microbial consortia and communities p. 101 Lipid analyses for viable microbial biomass, community composition, metabolic status, and in situ metabolism p. 112 Physiological profiling of microbial communities p. 126 Molecular approaches for the measurement of density, diversity, and phylogeny p. 139 Phylogenetic and genomic analysis p. 157 Bioreporters, biosensors, and microprobes p. 169 Ecology at long-term research sites : integrating microbes and ecosystems p. 182 Quality assurance p. 190 Issues of study design and statistical analysis for environmental microbiology p. 199 Overview of water microbiology as it relates to public health p. 219 Waterborne transmission of infectious agents p. 222 Detection of microorganisms in environmental freshwaters and drinking waters p. 249 Detection of protozoan parasites in source and finished drinking water p. 265 Microbial indicators of marine recreational water quality p. 280 Detection of viruses in environmental waters, sewage, and sewage sludges p. 290 Detection of bacterial pathogens in wastewater and sludge p. 300 Detection of pathogenic bacteria, viruses, and parasitic protozoa in shellfish p. 311 Control of microorganisms in source water and drinking water p. 325 Assessing the efficiency of wastewater treatment p. 334 Modeling the fate of microorganisms in water, wastewater, and soil p. 355 Estimating the risk of infectious disease associated with pathogens in drinking water p. 365 Toxic photosynthetic microbes p. 378 An overview of methodologies in aquatic microbial ecology p. 393 Cultivating microorganisms from dilute aquatic environments : melding traditional methodology with new cultivation techniques and molecular methods p. 399 Primary productivity and producers p. 407 Bacterial secondary productivity p. 421 Community structure : bacteria and archaea p. 434 Viral community structure p. 445 Protistan community structure p. 454 Decomposition and fungal community structure in aquatic environments p. 469 Bacterial organic carbon cycling in aquatic environments p. 479 Environmental genomics of C[subscript 1] metabolism p. 488 Sulfur cycling p. 497 Nitrogen cycling in aquatic environments p. 511 The marine phosphorus cycle p. 523 Microbial metal cycling in aquatic environments p. 540 Biofilms on living surfaces p. 563 Extreme high-pressure marine environments p. 575 Introduction and overview : soil, rhizosphere, and phyllosphere p. 595 Surface soil microbial sampling methods p. 597 Application of phylogenetic techniques in studies of soil microbial communities p. 608 Sampling viruses from soil p. 618 Isolation, culture, and detection of arbuscular mycorrhizal fungi p. 627 Isolation, in planta detection, and uses of endophytic bacteria for plant protection p. 638 Methods of soil microbial community analysis p. 652 Microarrays : design and use for agricultural and environmental applications p. 663 PCR : agricultural and environmental applications for soil microbes p. 676 Quantification of nitrogen transformations p. 687 Quantifying the metabolic activity of soil- and plant-associated microbes p. 697 Soil enzymes : linking proteomics and ecological processes p. 704 Immunofluorescence microscopy and fluorescence in situ hybridization combined with CMEIAS and other image analysis tools for soil- and plant-associated microbial autecology p. 712 Reporter gene systems useful in evaluating in situ gene expression by soil- and plant- associated bacteria p. 734 Identifying microorganisms involved in specific in situ functions : experimental design considerations for rRNA gene-based population studies and sequence-selective PCR assays p. 748 Mobile gene elements in environmental microbial communities p. 758 Microorganisms associated with soil arthropods p. 769 Lipid fingerprinting of soil microbial communities p. 781 Overview of issues in subsurface and landfill microbiology p. 795 Drilling, coring, and sampling subsurface environments p. 799 Anaerobic decomposition of refuse in landfills and methane oxidation in landfill covers p. 818 Biogeochemistry of aquifer systems p. 843 Determining the terminal electron-accepting reaction in the saturated subsurface p. 860 Transport of microorganisms in the terrestrial subsurface : in situ and laboratory methods p. 872 Oil field microbiology p. 898 Placement of drinking water wells and their protection p. 912 Introduction to aerobiology p. 925 Sampling for airborne microorganisms p. 939 Analysis of bioaerosol samples p. 952 Fate and transport of microorganisms in air p. 961 Airborne fungi and mycotoxins p. 972 Airborne bacteria and endotoxin p. 989 Legionellae and Legionnaires' disease p. 1005 Airborne viruses p. 1016 Aerobiology of agricultural pathogens p. 1031 Overview : biotransformation and biodegradation p. 1051 Functional gene arrays for microbial community analysis p. 1052 Methods for soil metagenomics : extraction and cloning of soil DNA p. 1063 Using genetic algorithms to optimize functions of microbial ecosystems p. 1072 Metagenomic methods for the identification of active microorganisms and genes in biodegradation processes p. 1079 Proteomic analysis of extracellular enzymes produced by wood-degrading fungi p. 1089 Current progress in the application of mycoremediation to soil cleanup p. 1097 Fungal solid-state fermentation systems for bioconversion of lignocellulosic biomass : process protocol and applications p. 1107 Characterization of microeukaryota in natural environments p. 1112 Methods useful in assessing biological and chemical activity of low-molecular-weight brown rot fungal metabolites p. 1122 Techniques for studying uncultured and cultured magnetotactic bacteria p. 1129 Growth of electrode-reducing bacteria p. 1137 Microbially mediated anaerobic iron(II) oxidation at circumneutral pH p. 1147 Isolation, enumeration, growth, and preservation of acidophilic prokaryotes p. 1155 Molecular techniques for the study of toxic metal resistance mechanisms in bacteria p. 1166 Synchrotron-based techniques for monitoring metal transformations p. 1183 Techniques for studying microbial transformations of metals and radionuclides p. 1195 Arsenate-respiring bacteria p. 1214 Biotransformations of manganese p. 1223 Microbial Fe(III) reduction : ecological and physiological considerations p. 1239 Author Index 1249 Subject Index 1251