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Environmental Microbiology and Microbial Ecology

Environmental Microbiology and Microbial Ecology

Larry L. Barton, R.J.C. McLean

ISBN: 978-1-118-96626-6

Mar 2019, Wiley-Blackwell

480 pages

Select type: Hardcover

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$129.95

Description

Microbial Ecology 2e covers the ecological activities of microbes in the biosphere with an emphasis on microbial interactions within their environments and communities, and provides insights into relevant methodologies for characterization of microorganisms in the environment.  In thirteen concise and timely chapters, the book presents a broad overview of this rapidly growing field, explaining the basic principles in an easy-to-follow manner.  Using an integrative approach, it comprehensively covers traditional issues in ecology as well as cutting-edge content at the intersection of ecology, microbiology, environmental science and engineering, and molecular biology.  The primary focus is on the single cell forms of prokaryotes (bacteria and archaea) with additional attention to cellular forms of algae, fungi and protozoans.  The book provides factual information and seeks to stimulate the reader by suggesting areas where research is incomplete and additional focus is needed.  Through the use of "Spotlights" the contribution or activities of several senior microbial ecologists are highlighted and these spotlights serve to emphasize the diversity of research avenues in microbial ecology.  These features make this an ideal textbook for graduate or upper-level undergraduate students in biology, microbiology, ecology, or environmental science.  It also serves as a highly useful reference for scientists and environmental professionals.

The authors draw upon their extensive experience in teaching microbiology to address the latest hot-button topics in the field, such as:
• Ecology of microorganisms in natural and engineered environments
• Advances in molecular-based understanding of microbial phylogeny and interactions
• Microbially driven biogeochemical processes and interactions among microbial populations and communities
• Microbial activities in extreme or unusual environments
• Ecological studies pertaining to animal, plant, and insect microbiology
• Microbial processes and interactions associated with environmental pollution

Reasons for a second edition: Our knowledge of the microbial world and microbial interactions within the environment (Microbial Ecology) is rapidly changing and it is necessary to provide the latest information and literature sources for these areas. Since there were some delays in getting the manuscript ready for publishing, some of the references are now somewhat dated. Most importantly, the chapter (Chapter 5) concerning methodologies for assessing microbial communities and community relationships needs to be addressed and this chapter will be the focus of our greatest changes of the existing text. Two additional chapters are proposed that would cover communication (oral and written) in the area of microbial ecology. Since undergraduate/initial graduate level courses often require research proposals, a short chapter addressing the writing, review of scientific research articles and presentation of ideas would be new to this book.  Communicating research findings to public audiences has become increasingly important and a chapter putting forth best techniques for public audience communication will be included.

Chapter 1. Introduction to Microorganisms and their Activities

Abstract

1.1 Central theme of environmental microbiology and microbial ecology

1.2 Are the terms prokaryotes and eukaryotes relevant?

1.2.1 Intracellular membranes in prokaryotes

1.2.2 Compartmentalized heterotrophic bacterial cells

1.2.3 The universal Tree of Life: rooted or unrooted

1.2.4 What about the giant viruses?

1.3 Major approach to study microorganisms

1.3. 1 Application of genomics, metagenomics and proteonomics

1.3. 2 Biochemical and physiological analysis

1.4 The impact of horizontal gene transfer between microorganisms.

1.4.1 Genetic islands

1.4.2 Risks from genetically modified organisms

1.4.3 Microbial viruses and gene transfer agents

1.5 What determines which microorganisms are present?

1.5.1. Metabolism as a basis of selection

1.5.2 Is persistence of microorganisms dependent only on spore production?

1.6 Is the size and shape of a prokaryotic cell important?

1.6.1 Nanobacteria

1.6.2 Ultramicroscopic bacteria

1.6.2 Very large bacteria

1.6.3 Influence of diffusion on bacterial cell form

1.6.4 Features of a specific cell form

1.6.4.1 Coccus form

1.6.4.2 Rod form

1.6.4.3 Curved rod or spirochete form

1.6.4.4 Unusual forms

1.7 Microbial predation

1. 7.1 Bacteria as prey

1. 7.2 Bacteria as trackers and predators

1.8 Summary

Discussion Questions

BIBLOGRAPHIC MATERIAL

Suggested Reading

Cited References

Chapter 2 Microbes in the Biosphere: Examination, Cultivation and Communities

Abstract

2.1 Overview and focus

2.2 Microscopy to study environmental microbes

2.2.1 Light supported microscopy

2.2.2 Fluorescence microscopy

2.2.3 Scanning confocal laser microscopy

2.2.4 High resolution by electron microscopy

2.3 Internal structures in prokaryotes

2.3.1 Gas vacuoles

2.3.2 Sulfur globules

2.3.3 Polymeric carbon reserves

2.3.4 Polyphosphate granules

2.3.5 Metallic nanoparticles

2.4 Strategies for culturing microorganisms

2.4.1 Overview

2.4.2 Approaches for isolation of microorganisms

2.4.3 Establishing microbial communities

2.4.4 The iChip and growing uncultured bacteria

2.5 Molecular detection

2.5.1 Characterization of microorganisms using genomics and metagenomics

2.5.2 Physiological analysis using metatranscriptomics and metaproteomics

2.5.3 Lipid biomarker profiles

2.6 Examining bacteria that do not grow as pure cultures in the laboratory

2.6.1 Host-dependent microorganisms

2.6.1.1 Bacteria as obligate pathogens

2.6.1.2 Bacteria as endosymbionts

2.6.1.3 The Nanoarchaeum – Ignicoccus relationship

2.6.2 Molecular analysis of uncultivable bacteria

2.7 Microbial community structures

2.7.1 Primary production and microbial communities

2.7.2 Biofilms

2.7.3 Role of quorum sensing

2.8 Summary

Discussion Questions

BIBLOGRAPHIC MATERIAL

Suggested Reading

Cited References

Chapter 3 Terrestrial systems: Soil and Subsurface Environments

Abstract

3.1 Overview and focus

3.2 Soil: an environment for microorganisms

3.2.1 Soil horizons

3.2.2 Soil organic matter (SOM)

3.3 Soil Microbiology

3.3.1 Soil prokaryotes

3.3.2 Soil fungi

3.3.3 Soil crusts

3.3.4 Soil invertebrates and burrowing animals

3.3.5 The rhizosphere and associated bacteria

3.4 Understanding soil ecosystems

3.4.1 The Carbon:Nitrogen ratio

3.4.2 The Fungi:Bacteria ratio

3.4.3 SOM and soil food web

3.4.4 Influence of agricultural management on soil microbe community

3.4.5 Impact of viruses on the soil microbiota

3.5 Subsurface microbiology

3.5.1 Groundwater

3.5.2 Cave water

3.5.3 Deep subsurface aquifers

3.5.3.1 Aquifer in a coal-bearing basin

3.5.3.2 Deep granitic aquifer

3.5.3.3 Anaerobic, alkaline aquifer

3.5.3.4 Saline hydrothermal aquifer

3.6 Deep subsurface microbiology

3.6.1 Marine sediment microbiology

3.6.2 Deep mines and boreholes

3.6.3 Deep subseafloor

3.6.4 Deep subsurface storage sites

3.6.4.1 Storage of nuclear fuel waste

3.6.4.2 Underground storage for H2 and CH4

3.6.4.3 Underground storage for CO2

3.6.4.4 Geothermal energy production

3.6.5 Endolithic microorganisms

3.7 Life in deep subsurfaces

3.7.1 Adjusting to a subsurface diet

3.7.2 Energy sources in the deep biosphere

3.7.3 The benefit of living together

3.8 Geomicrobiology

3.8.1 Rock and mineral weathering

3.8.2 Mineral transformations

3.8.3 Microbial metal binding

3.8.4 Microbiota of subsurface crystals

3.9 Summary

Discussion Questions

BIBLOGRAPHIC MATERIAL

Suggested Reading

Cited References

Chapter 4 Aquatic Surface Environments: Freshwater, Marine and Wastewater

Abstract

4.1 Overview

4.2 Water as relevant to microbial growth

4.2.1 Water activity

4.3 Marine environments and associated microbiomes

4.3.1 Marine primary productivity

4.3.2 Marine heterotrophs

4.3.3 Bacterial symbionts and marine hosts

4.3.4 Microbial EPSs, marine snow and marine gel particles

4.3.5 Brackish water and intertidal zones

4.3.6 Coral reefs

4.4 Freshwater environments and associated microbiomes

4.4.1 Lakes and rivers

4.4.2 Wetlands

4.4.3 The snow and glacier ice ecosystems

4.4.4 Microbiota of cold and hot springs

4.4.5 Microbial mats

4.5 Maintaining populations in low nutrient environments

4.6 Aquaculture wastewater

4.7 Hormone degradation in fresh water

4.8 Human activities and influence on microbial ecology

4.9 Drinking water

4.10 Municipal water treatment

4.11 Wastewater treatment systems

4.11.1 Septic tanks

4.11.2 Municipal wastewater treatment

4.11.2.1Primary treatment

4.11.2.2 Secondary treatment

4.12 Alternative approaches for wastewater treatment

4.13. Coliforms and other indicator organisms

4.14 Virus in aquatic environments: diversity and activity

4.15 Summary

Discussion Questions

BIBLOGRAPHIC MATERIAL

Suggested Reading

Cited References

Chapter 5 – Life in Extreme Environments

Abstract

5.1 Overview

5.2 Sampling in an extreme environment

5.3 Extreme temperature environments

5.3.1 Psychrophiles

5.3.2Thermophiles

5.3.2.1 Alpine environment – Yellowstone National Park

5.3.2.2 Hydrothermal vent communities

5.3.2.3 The Guaymas Basin

5.4 Xerophiles

5.5 Piezophiles

5.6 Acidophiles

5.7 Alkaliphiles

5.8 Halophiles and chaophiles

5.9 Radioresistant microorganisms

5.10 Membrane adaptations to extreme conditions

5.10.1 Low temperature

5.10.2 High temperatures

5.10.3 pH extremes: low and high

5.11 Astrobiology

5.12 Nutrient limited environments

5.13 Volcanic surfaces

5.14 Summary

Discussion Questions

BIBLOGRAPHIC MATERIAL

Suggested Reading

Cited References

Chapter 6. Mutualism: Microorganisms and Terrestrial Plants

Abstract

6.1 Overview and focus

6.2 Cyanobacteria and the chloroplast ancestor

6.3 Lichens: cyanobacteria/algae – fungi mutualism

6.3.1 Distribution and organization

6.3.2 Natural products of lichens

6.4. Mutualisms with cyanobacteria as intracellular or epiphytic organisms

6.4.1 Bryophytes

6.4.2 Mosses

6.4.3 Azolla

6.4.4 Gunnera

6.4.5 Cycads

6.4.6 Geosiphon

6.4.7 Diatoms

6.5 Rhizobia – legume symbiosis

6.5.1 Bacterial species involved

6.5.2 Rhizospheric rhizobia

6.5.3 The root nodulation process

6.5.4 Nodules on plant stems

6.6 Frankia and the non-legume nitrogen-fixing nodule

6.7 Mycorryzae

6.7.1 Arbuscular mycorrhizae (AM)

6.7.2 Ectomycorrhiza (EcM)

6.8 Patterns of regulation for plant-microbe mutalism

6.9 Bacterial-fungal interactions

6.9.1 Direct effects

6.9.2 Plant growth-promoting bacteria

6.9.3 Systemic induction of plant immunity

6.10 Endophytic microorganisms

6.11 Microbiology of the phyllosphere

6.12 Summary

Discussion Questions

BIBLOGRAPHIC MATERIAL

Suggested Reading

Cited References

Chapter 7. Mutualism: Microorganisms and Animals

Abstract

7.1 Overview and focus

7.2 Building a microbial community – the role of the host

7.2.1 Microbiology and innate immunity

7.2.2 Microbiology and adaptive immunity

7.3 Host models to study parasite relationships

7.3.1 Germ-free animals

7.3.2 Caenorhabditis elegans

7.3.3 Drosophila melanogaster

7.3.4 Galleria mellonella

7.4 Digestive tract environment

7.4.1 Omnivores

7.4.2 Carnovores

7.4.3 Herbivores

7.4.3.1 Bacteria and archaea

7.4.3.2 Anaerobic protozoa

7.4.3.3 Anaerobic fungi

7.4.3.4 Probiotics and methane mitigation strategies

7.5 The Human microbiome

7.5.1 Skin

7.5.2 Oral

7.5.3 Intestinal microbiome

7.5.3.1 Establishment of intestional flora

7.5.3.2 The healthy gut

7.5.3.3 Influence of the intestine on human health

7.5.3.4 Obesity, diabetes and health issues.

7.5.3.5 Probiotics

7.6 Gut microbiota across the animal world

7.6.1 Systems of maternal transmission

7.6.2 Microbiota of ruminates and hindgut fermenters

7.6.3 Gut microbiota in bears

7.6.4 Microbiota of birds

7.6.5 Intestinal bacteria of fish

7.7 Insect-fungus symbiosis

7.7.1 Scale insects and Septobasidium

7.7.2 Attine ant - fungus symbiosis

7.7.3 Woodwasp - fungus symbiosis

7.7.4 Ambrosia beetles – fungus

7.7.5 Termite - fungus

7.8 Mutualisms involving insects and bacteria

7.8.1Aphids - Buchnera

7.8.2Wolbachia – insects

7.8.3Mealybug – bacteria

7.8.4Termite gut - bacteria

7.9 Muturalisms involving invertebrates

7.9.1 Microbiome of marine worms

7.9.2 Squid (Euprymna) – Vibrio fischeri symbiosis

7.9.3 Medical leech - Aeromonas sp. and Ricenella-like bacteria

7.9.4 Nematode – bacteria

7.10 Summary

Discussion Questions

BIBLOGRAPHIC MATERIAL

Suggested Reading

Cited References

Chapter 8. Microbes Driving the Nutrient Cycles

Abstract

8.1. Overview and focus

8.2. Nutrient cycles and what drives them

8.3. The aerobic environment

8.3.1 The “Great Oxidation Event”

8.3.2 Oxygen cycle

8.3.3 Hydrogen peroxide and ROS

8.4. Carbon a renewable resource

8.4.1 Carbon dioxide fixation and carbonate reduction

8.4.2 Methanogenesis, methanotrophy and methylotrophy

8.4.3 Mineralization of carbon compounds

8.4.4 Production and utilization of CO

8.4.5 Production and utilization of hydrogen cyanide (HCN)

8.5. Nitrogen for biosynthesis and energy

8.5.1 Nitrification

8.5.2 Denitrification

8.5.3 Nitrate reduction

8.5.4 Nitrite reductase

8.5.5 Metabolism of NO and N2O

8.5.6 Production of NO by NOS

8.5.7 Respiratory ammonification

8.5.8 Anammox reaction

8.5.9 Assimilation of nitrogen

8.5.10 Dinitrogen fixation

8.6. Sulfur cycling

8.6.1 Oxidation of hydrogen sulfide

8.6.2 Oxidation of elemental sulfur

8.6.3 Dissimilative S0 reduction

8.6.4 Dissimilative sulfate reduction

8.6.5 Assimilatory sulfate reduction

8.6.6 Production of H2S and dimethyl sulfide, (CH3)2S

8.6.6.1 Hydrogen sulfide

8.6.6.2 Dimethyl sulfide

8.7. Cycling of trace elements

8.7.1 Iron

8.7.2 Manganese

8.8. Phosphorus cycling

8.9. Selenium cycling

8.10. Cycling toxic elements

8.10.1 Mercury

8.10.2 Arsenic

8.11 Summary

Discussion Questions

BIBLOGRAPHIC MATERIAL

Suggested Reading

Cited References

Chapter 9. Bioremediation using Microorganisms

Abstract

9.1 Overview and focus

9.2 Microbial bioremediation: strategies and applications

9. 2. 1 Biostimulation

9. 2. 2 Bioagumentation

9.2.2.1 Indigenous bacteria

9.2.2.2 Genetically modified organisms

9. 2. 3 Intrinsic bioremediation

9. 2. 4 Microbial consortium

9. 2. 5 Co-metabolism

9. 3 Organic compounds and xenobiotics degraded

9. 3. 1 Pesticides

9. 3. 2 Chlorinated organic compounds

9. 3. 2. 1 Chloroethylenes

9. 3. 2. 2 Chloromethanes

9. 3. 2. 3 Polychlorinated biphenyl compounds

Anaerobic dehalogenation

Aerobic metabolism

9. 3. 3 Population dynamics in degradation of hydrocarbons

9. 3. 3. 1 Oil spills

9. 3. 3. 2 Fuel hydrocarbons

9. 3. 3. 3 Polyaromatic hydrocarbon (PAH)

9. 3. 3. 4 Azo dyes

9. 3. 4 Explosives

9. 3. 4. 1 Trinitrotoluene.

9. 3. 4. 2 RDX and HMX

9. 3. 4. 3 Perchlorate

9. 3. 5 Bioremediation and detoxification of metal(loid)

9. 3. 5. 1 Dissimilatory metal(loid) reduction

9. 3. 5. 2 Immobilization by binding

9. 4 Design of systems for bioremediation

9. 4. 1 In situ vs ex situ

9. 4. 2 Bioreactors

9. 4. 3 Biofarming

9. 4.4 Permeable reactive barriers

9. 4. 5 Groundwater and lagoon treatment

9. 4. 6 Bioventing

9.5 Summary

Discussion Questions

BIBLOGRAPHIC MATERIAL

Suggested Reading

Cited References

Chapter 10. Biocorrosion and Geomicrobiology

Abstract

10.1 Introduction

10.2. Microbially influenced corrosion (MIC) of ferrous metals

10.2.1 Current theories of biocorrosion

10.2.1.1 EMIC

10.2.1.2 CMIC

10.2.1.3 Iron sulfide crusts

10.2.1.4 Biofilms and extracellular matrix

10.2.2 Biocorrosion of nonferrous materials

10.2.3 Control of biocorrosion

10.3 Bioalteration of rocks, monuments and other surfaces

10.3.1 Biofilms on rocks and buildings

10.3.2 Biodegradation of art objects

10.3.2.1 Marble statues in Italy

10.3.2.2 Paintings in the Lascaux Cave in France

10.3.2.3 Mogao Grottoes in China

10.3.2.4 Damage to frescoes

10.3. 3 Biotechnology for restoration of artworks and historic stones

10.4 Biodeterioration of concrete

10.5 Mineral interaction and biomineralization

10.5.1 Iron hydroxides

10. 5.2 Magnetic mineral crystals

10. 5. 3 Manganese oxides

10. 5. 4 Carbonates

10. 5. 5 Phosphates

10. 5. 6 Sulfates

10. 5. 7. Sulfides

10. 5. 8 Clays

10. 5. 10 Uranium precipitate and crystals

10. 5. 11 Gold grains

10.6 Interactions with transition and rare earth elements

10. 6. 1 Transition elements

10. 6. 2 Rare earth elements.

10. 7 Toxic elements

10. 7. 1 Mercury

10. 7. 2 Chromium

10. 7. 3 Arsenic

10. 7. 4 Selenium

10.8 Metallic and metalloid nanoparticles of microbial origin

10.9 Summary

Discussion Questions

BIBLOGRAPHIC MATERIAL

Suggested Reading

Cited References

Chapter 11. Microbial Communities and Metabolic Networks

Abstract

11.1 Introduction and focus

11.2 Examples of succession of populations

11.2.1 Development of coral black band disease

11.2.2 Population succession in production of dairy products

11.2.3 Population dynamics in fermentation of non-dairy foods

11.2.3.1 Kimchi

11.2.3.2 Coffee

11.2.3.3 Cocoa

11.2.3.4 Chinese soy sauce

11.2.4 Composting plant material

11.3 Impact of climate change on microorganisms

11.3.1 Marine environment

11.3.2 Soil environment

11.4 Syntrophy and co-metabolism

11.5 Ecosystem created by hydraulic fracturing in shale

11.6 Extracellular electron transport

11.6.1 Membrane-bound proteins

11.6.2 Electron shuttling

11.6.3 Nanowires

11.6.4 Extracellular electron movement in biofilms

11. 7 Cross talk: Interkingdom signaling

11.7.1 Microbial endocrinology

11.7 2 Cross signaling in nonhuman systems

11.8 Evolving systems of interest

11.8.1 Polyplody in bacteria

11.8.2 Impact of viruses and CRISPR-cas systems

11.8.3 Impact of outer membrane vesicles

11.8.4 Atmospheric microbiology

11.8.5 Long-distance electron transfer

11.9 Summary

Discussion Questions

BIBLOGRAPHIC MATERIAL

Suggested Reading

Cited References

Index