Note: Cover -- Processes in Microbial Ecology -- Copyright -- Preface -- Table of Contents -- CHAPTER 1. Introduction -- What is a microbe? -- Why study microbial ecology? -- Microbes cause diseases of macroscopic organisms, including humans -- Microbes help to make our food and other useful products -- Microbes degrade and detoxify pollutants -- Microbes are models for exploring principles in ecology and evolution -- Microbes living today are models for early life on Earth and perhaps life on other planets -- Microbes mediate biogeochemical processes that affect global climate -- Microbes are everywhere, doing nearly everything -- How do we study microbes in nature? -- Separating microbes by phylogeny: the three domains of life -- Separating microbes into functional groups -- Autotroph versus heterotroph -- Phototroph versus chemotroph -- Combining structure and function -- Summary -- CHAPTER 2. Elements, biochemicals, and structures of microbes -- Elemental composition of microbes -- Elemental ratios in biogeochemical cycles .and studies -- C:N and C:P ratios for microbes -- Biochemical composition of microbes -- Variation in elemental ratios and biochemical composition -- Architecture of a microbial cell -- Membranes of microbes and active transport -- Cell walls in prokaryotes and eukaryotes -- Components of microbial cells as biomarkers -- Extracellular structures -- Extracellular polymers of microbes -- Flagella and cilia -- fimbriae and pili -- Summary -- CHAPTER 3. The physical-chemical environment of microbes -- Some important physical-chemical properties -- Water -- Temperature -- pH -- Salt and osmotic balance -- Oxygen and redox potential -- Light -- Pressure -- The consequences of being small -- Microbial life in natural aquatic habitats -- Motility and taxis -- Submicron- and micron-scale patchiness in aqueous environments. , Microbial life in soils -- Water content of soils -- Interactions between temperature and water content in soils -- The biofilm environment -- Summary -- CHAPTER 4. Community structure of microbes in natural environments -- Taxonomy and phylogeny via genes: introduction to 16S rRNA-based methods -- The species problem -- Terms of diversity -- Patterns of diversity -- Bacterial communities are diverse but very uneven -- Uncultivated bacteria are not the same as easily cultivated bacteria -- Different bacteria are found in soils, freshwaters, and the oceans -- A few bacteria are widely distributed -- Archaea in non-extreme environments -- Ecological processes that assemble microbial communities -- Deterministic versus stochastic processes -- Everything everywhere? -- What controls diversity levels and bacterial community structure? -- Oxygen, temperature, salinity, and pH -- Moisture and soil microbial communities -- Organic material and inorganic nutrients -- Predation and viral lysis -- Community structure of fungi -- Relevance of community structure to understanding processes -- Summary -- CHAPTER 5. Genomes and meta-omics for microbes -- What are genomics and environmental genomics? -- Turning genomic sequences into genomic information -- Lessons from cultivated microbes -- Similar rRNA genes, dissimilar genomes -- Core genomes and pangenomes -- Genome size -- Organization of eukaryotic versus prokaryotic genomes -- Horizontal gene transfer -- Genomes and growth strategies for bacteria -- Specific genomic features and growth -- Streamlined genomes -- Oligotrophic versus copiotrophic bacterial genomes -- Genomes from uncultivated microbes: metagenomics -- Metagenomic approaches and linking structure with function -- Single-cell genomics -- Metatranscriptomics and metaproteomics -- Transcriptional response of oligotrophic and copiotrophic bacteria. , Metatranscriptomes of eukaryotic microbes -- Summary -- CHAPTER 6. Microbial primary production and phototrophy -- Basics of primary production and photosynthesis -- The carbon dioxide-fixing enzyme -- Primary production, gross production, and net production -- Primary production by terrestrial higher plants and aquatic microbes -- The spring bloom and controls of phytoplankton growth -- Major groups of bloom-forming phytoplankton -- Diatoms -- Phaeocystis and dimethylsulfide -- Cyanobacteria and filamentous diazotrophs -- After the bloom: competition for limiting nutrients -- Primary production by coccoid cyanobacteria -- Anaerobic anoxygenic photosynthesis -- Sessile algae and microbial mats -- Summary -- CHAPTER 7. Degradation of organic matter -- Who does most of the respiration on the planet? -- Detritus and detrital food webs -- DOM and the microbial loop -- Bacterial growth efficiency and carbon use efficiency -- Mechanism of organic matter degradation -- Hydrolysis of high molecular weight organic compounds -- Uptake or mineralization of N and P? -- Degradation of lignin and other higher plant compounds -- Interactions between organic compounds: protection and priming -- Protection by adsorption or aggregation -- Priming effects -- Photoheterotrophy: energy from organic material and light -- Contribution of microbes to ancient organic carbon and SOM formation -- Degradation and microbial diversity -- Summary -- CHAPTER 8. Microbial growth, biomass production, and controls -- Are microbes alive or dead? -- Activity state of bacteria in water and soils -- Activity state of individual bacterial taxa -- Introduction to growth and biomass production -- Growth in the laboratory: batch cultures -- Growth in the laboratory: continuous cultures -- Maintenance energy -- Growth rates and biomass production in nature. , Growth rates of phytoplankton, bacteria, and fungi -- Growth rates of individual microbial taxa -- Growth in the deep biosphere -- What sets growth by heterotrophic microbes in nature? -- Temperature effects on growth and carbon cycling -- pH effects -- Soil moisture -- Limitation by organic carbon -- Limitation by inorganic nutrients -- Co-limitation and interactions between controlling factors -- Cooperation between organisms -- Summary -- CHAPTER 9. Predation and protists -- Bacterivory in aquatic habitats -- Grazers of bacteria and fungi in soils and sediments -- Mechanism of protist grazing -- Factors a˛ecting grazing -- Prey number and predator-prey cycles -- Size relationships of predator and prey -- Chemical recognition and composition -- Grazing by larger protists: ciliates and dinoflagellates -- Ciliates as predators of bacteria, flagellates, and fungi -- Heterotrophic dinoflagellates -- Mixotrophic protists and endosymbiosis -- Protist community structure and the evolution of eukaryotes -- Exploring protist community structure -- Biogeography of protists -- Connecting protist communities with processes -- Summary -- CHAPTER 10. The ecology of viruses -- What are viruses? -- The number of viruses in natural environments -- Counting viruses by the plaque assay -- Counting viruses by microscopy -- Virus-bacteria ratio in nature -- Viral replication -- Temperate viruses and lysogeny in nature -- Host range of viruses -- Viral production, loss, and mortality of bacteria -- Percentage of infected cells -- Contribution of viruses versus grazers to bacterial mortality -- Viral decay and loss -- Viruses are not grazers -- Viral shunt and DOM production -- Population dynamics of a virus and its host -- Genetic exchange mediated by viruses -- Metagenomics of viruses -- Viral diversity -- Core, noncore, and auxiliary metabolic genes. , Viruses of other organisms -- Mycoviruses: Viruses in fungi -- Viruses infecting algae and amoebae -- Summary -- CHAPTER 11. Processes in anoxic environments -- Introduction to anaerobic respiration -- Microbes use electron acceptors in order of redox potential -- Oxidation of organic carbon by di˛erent electron acceptors -- Limitations by concentration and supply -- Effect of physical state and chemical form -- The anaerobic food chain -- Fermentation -- Acetogenesis, interspecies hydrogen transfer, and syntrophy -- The sulfur cycle and sulfate reduction -- Electron donors for sulfate reduction -- Oxidation of reduced sulfur compounds and the rest of the sulfur cycle -- Non-phototrophic sulfur oxidation -- Sulfide oxidation by anoxygenic photosynthesis -- The carbon source for sulfur oxidizers -- Methane and methanogenesis -- Methanotrophy -- Aerobic methane degradation -- Anaerobic methane oxidation -- Anaerobic microbial eukaryotes -- Summary -- CHAPTER 12. The nitrogen cycle -- Nitrogen fixation -- Nitrogenase, the N2-fixing enzyme -- Solving the oxygen problem -- N2 fixation in nature -- Limitation of N2 fixation -- Ammonium assimilation, regeneration, and fluxes -- Ammonia oxidation and nitrification -- Aerobic ammonia oxidation by bacteria -- Ammonia oxidation by archaea -- Controls of aerobic ammonia oxidation -- The second step in nitrification: nitrite oxidation -- Complete nitrification by one organism -- Dissimilatory nitrate reduction and denitrification -- Anaerobic ammonia oxidation -- Denitrification versus anaerobic ammonia oxidation -- Sources and sinks of nitrous oxide -- Production by bacteria and archaea -- Consumption of N2O -- N budgets: global balance, local imbalances -- Summary -- CHAPTER 13. Introduction to geomicrobiology -- Cell surface charge and metal sorption -- Biomineralization by microbes. , Iron minerals and microbes.