Environmental Microbiology and Microbial Ecology

Larry L. Barton is Professor Emeritus, Department of Biology, University of New Mexico. He is author or co-editor of eight books on microbiology and is founding editor of the journal Anaerobe. Dr. Barton studies the physiological activities of microorganisms, focusing on energetics of anaerobic bacteria and bacterial inorganic metabolism. R.J.C. McLean is Regents Professor, Department of Biology, Texas State University. His research include biofilm growth and development as well as microbial mineral formation and nanobacteria.

Preface xv 1 Introduction to Microorganisms and Their Activities 1 1.1 Central Themes of Environmental Microbiology and Microbial Ecology 1 1.2 Are the Terms Prokaryotes or Eukaryotes Relevant? 1 1.2.1 Intracellular Membranes in Prokaryotes 2 1.2.2 Compartmentalized Heterotrophic Bacterial Cells 3 1.2.3 The Universal Tree of Life: Rooted or Unrooted 4 1.2.4 What About the Giant Viruses? 4 1.3 Major Approach to Study Microorganisms 5 1.3.1 Application of Genomics, Metagenomics, and Proteomics 6 1.3.2 Biochemical and Physiological Analysis 7 1.4 The Impact of Horizontal Gene Transfer Between Microorganisms 7 1.4.1 Genetic Islands 9 1.4.2 Risks from Genetically Modified Organisms 10 1.4.3 Microbial Viruses and Gene Transfer Agents 10 1.5 What Determines Which Microorganisms are Present? 12 1.5.1 Metabolism as a Basis of Selection 13 1.5.2 Is Persistence of Microorganisms Dependent Only on Spore Production? 14 1.6 Is the Size and Shape of a Prokaryotic Cell Important? 19 1.6.1 Nanobacteria 19 1.6.2 Ultramicroscopic Bacteria 21 1.6.3 Very Large Bacteria 21 1.6.4 Influence of Diffusion on Bacterial Cell Form 22 1.6.5 Features of a Specific Cell Form 22 1.6.5.1 Coccus Form 22 1.6.5.2 Rod Form 22 1.6.5.3 Curved Rod or Spirochete Form 23 1.6.5.4 Unusual Forms 23 1.7 Microbial Predation 23 1.7.1 Bacteria as Prey 23 1.7.2 Bacteria as Trackers and Predators 24 1.8 Summary 25 Discussion Questions 25 References 26 Further Reading 31 2 Microbes in the Biosphere: Examination, Cultivation, and Communities 33 2.1 Overview and Focus 33 2.2 Microscopy to Study Environmental Microbes 33 2.2.1 Light Supported Microscopy 34 2.2.2 Fluorescence Microscopy 35 2.2.3 Scanning Confocal Laser Microscopy 37 2.2.4 High Resolution by Electron Microscopy 37 2.3 Internal Structures in Prokaryotes 41 2.3.1 Gas Vacuoles 41 2.3.2 Sulfur Globules 41 2.3.3 Polymeric Carbon Reserves 42 2.3.4 Polyphosphate Granules 43 2.3.5 Metallic Nanoparticles 43 2.4 Strategies for Culturing Microorganisms 44 2.4.1 Overview 44 2.4.2 Approaches for Isolation of Microorganisms 45 2.4.3 Establishing Microbial Communities 45 2.4.4 The iChip and Growing Uncultured Bacteria 46 2.5 Molecular Detection 49 2.5.1 Characterization of Microorganisms Using Genomics and Metagenomics 49 2.5.2 Physiological Analysis Using Metatranscriptomics and Metaproteomics 53 2.5.3 Lipid Biomarker Profiles 54 2.6 Examining Bacteria that Do Not Grow as Pure Cultures in the Laboratory 56 2.6.1 Hostdependent Microorganisms 56 2.6.1.1 Bacteria as Obligate Pathogens 56 2.6.1.2 Bacteria as Endosymbionts 57 2.6.1.3 The NanoarchaeumIgnicoccus Relationship 58 2.6.2 Molecular Analysis of Uncultivable Bacteria 58 2.7 Microbial Community Structures 59 2.7.1 Primary Production and Microbial Communities 59 2.7.2 Biofilms 62 2.7.3 Role of Quorum Sensing 64 2.8 Summary 67 Discussion Questions 68 References 68 Further Reading 75 3 Terrestrial Systems: Soil and Subsurface Environments 77 3.1 Overview and Focus 77 3.2 Soil: An Environment for Microorganisms 77 3.2.1 Soil Horizons 78 3.2.2 Soil Organic Matter (SOM) 78 3.3 Soil Microbiology 80 3.3.1 Soil Prokaryotes 80 3.3.2 Soil Fungi 82 3.3.3 Soil Crusts 83 3.3.4 Soil Invertebrates and Burrowing Animals 83 3.3.5 The Rhizosphere and Associated Bacteria 83 3.4 Understanding Soil Ecosystems 85 3.4.1 The Carbon : Nitrogen Ratio 85 3.4.2 The Fungi : Bacteria Ratio 85 3.4.3 SOM and Soil Food Webs 86 3.4.4 Influence of Agricultural Management on the Soil Microbe Community 89 3.4.5 Impact of Viruses on the Soil Microbiota 90 3.5 Subsurface Microbiology 90 3.5.1 Groundwater 90 3.5.2 Cave Water 92 3.5.3 Deep Subsurface Aquifers 92 3.5.3.1 Aquifer in a Coalbearing Basin 92 3.5.3.2 Deep Granitic Aquifer 93 3.5.3.3 Anaerobic, Alkaline Aquifer 94 3.5.3.4 Saline Hydrothermal Aquifer 94 3.6 Deep S