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- Herausgeber: John Wiley & Sons
- Kategorie: Wissenschaft und neue Technologien
- Sprache: Englisch
An updated text exploring the properties of the soil microbial community Today, the environmentally oriented specialties of microbiology are shifting from considering a single or a few microbial species to focusing on the entire microbial community and its interactions. The third edition of Soil Microbiology has been fully revised and updated to reflect this change, with a new focus on microbial communities and how they impact global ecology. The third edition still provides thorough coverage of basic soil microbiology principles, yet the textbook also expands students' understanding of the role the soil microbial community plays in global environmental health and human health. They can also learn more about the techniques used to conduct analysis at this level. Readers will benefit from the edition's expanded use of figures and tables as well as the recommendations for further reading found within each chapter. * Considers the impact of environmental perturbations on microbial community structure as well as the implications for soil system functions * Discusses the impact of soil microbial communities on food and health related issues * Emphasizes the importance of soil microbial communities on the sustainability of terrestrial ecosystems and solutions to global issues This third edition is a suitable text for those studying soil microbiology and soil ecology at the undergraduate or graduate level. It also serves as a valuable reference tool for professionals working in the fields of reclamation and soil management.
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Veröffentlichungsjahr: 2020
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Table of Contents
Cover
Title Page
Copyright Page
Preface
Introduction
1 Soil Ecosystems
1.1 Soil as an Ecosystem
1.2 The Micro‐ecosystem
1.3 The Macro‐ecosystem
1.4 Concluding Comments
References
2 The Soil Ecosystem
2.1 The Living Soil Component
2.2 Measurement of Soil Microbial Biomass
2.3 The Nature of Soil Inhabitants
2.4 Autecology and Soil Microbiology
2.5 Principles and Products of Synecological Research
2.6 Interphase Between Study of Individual and Community Microbiology
2.7 Concluding Comments
References
3 Microbial Diversity of Soil Ecosystems
3.1 Classical Culture‐Based Studies of Soil Microbial Diversity
3.2 Surrogate Measures of Soil Microbial Diversity
3.3 Diversity Surrogates: Physiological Profiling
3.4 Diversity Surrogates: Phospholipid Fatty Acid Analysis
3.5 Nucleic Acid‐Based Analyses of Soil Microbial Diversity
3.6 PCR‐Based Methods
3.7 Metagenomics
3.8 Conclusions: Utility and Limitations of Diversity Analysis Procedures
References
4 Energy Transformations Supporting Growth and Survival of Soil Microbes
4.1 Microbial Growth Kinetics in Soil
4.2 Microbial Growth Phases: Laboratory‐Observed Microbial Growth Compared to Soil Population Dynamics
4.3 Mathematical Representation of Soil Microbial Growth
4.4 Uncoupling Energy Production from Microbial Biomass Synthesis
4.5 Implications of Microbial Energy and Carbon Transformation Capacities for Soil Biological Processes
4.6 Concluding Comments
References
5 Process Control in Soil
5.1 Microbial Response to Abiotic Limitations: General Considerations
5.2 Impact of Individual Soil Properties on Microbial Activity
5.3 Microbial Adaptation to Abiotic Stress
5.4 Concluding Comments
References
6 Soil Enzymes
6.1 A Philosophical Basis for the Study of Soil Enzymes
6.2 Basic Soil Enzyme Properties
6.3 Principles of Enzyme Assays
6.4 Enzyme Kinetics
6.5 Distribution of Enzymes in Soil Organic Components
6.6 Ecology of Extracellular Enzymes
6.7 Concluding Comments
References
7 Microbial Interactions and Community Development and Resilience
7.1 Common Concepts of Microbial Community Interaction
7.2 Classes of Biological Interactions
7.3 Trophic Interactions and Nutrient Cycling
7.4 Importance of Microbial Interactions to Overall Biological Community Development
7.5 Management of Soil Microbial Populations
7.6 Concluding Comments: Implications of Soil Microbial Interactions
References
8 The Rhizosphere/Mycorrhizosphere
8.1 The Rhizosphere
8.2 Mycorrhizal Associations
8.3 The Mycorrhizosphere
8.4 Conclusion
References
9 Introduction to the Biogeochemical Cycles
9.1 Introduction to Conceptual and Mathematical Models of Biogeochemical Cycles
9.2 Specific Models of Biogeochemical Cycles and Their Application
9.3 Biogeochemical Cycles as Sources of Plant Nutrients for Ecosystem Sustenance
9.4 General Processes and Participants in Biogeochemical Cycles
9.5 Measurement of Biogeochemical Processes: What Data Are Useful?
9.6 Conclusions
References
10 The Carbon Cycle
10.1 Environmental Implications of the Soil Carbon Cycle
10.2 Biochemical Aspects of the Soil Carbon Cycle
10.3 Kinetics of Soil Carbon Transformations
10.4 Conclusions: Management of the Soil Carbon Cycle
References
11 The Nitrogen Cycle
11.1 Nitrogen Mineralization
11.2 Nitrogen Immobilization
11.3 Quantitative Description of Nitrogen Mineralization Kinetics
11.4 Microbiology of Mineralization
11.5 Environmental Influences on Nitrogen Mineralization
11.6 Nitrification
11.7 Concluding Observations: Control of the Internal Soil Nitrogen Cycle
References
12 Nitrogen Fixation
12.1 Biochemistry of Nitrogen Fixation
12.2 General Properties of Soil Diazotrophs
12.3 Conclusions
References
13 Biological Nitrogen Fixation
13.1 Rhizobium–Legume Symbioses
13.2 Manipulation of
Rhizobium
–Legume Symbioses for Ecosystem Management
13.3 Rhizobial Inoculation Procedures
13.4 Nodule Occupants: Indigenous vs Foreign
13.5 Actinorhizal Associations
13.6 Conclusions
References
14 Denitrification
14.1 Pathways for Biological Reduction of Soil Nitrate
14.2 Biochemical Properties of Denitrification
14.3 Environmental Implications of Nitrous Oxide Formation
14.4 Microbiology of Denitrification
14.5 Quantification of Nitrogen Losses from an Ecosystem via Denitrification
14.6 Environmental Factors Controlling Denitrification Rates
14.7 Conclusions
References
15 Fundamentals of the Sulfur, Phosphorus, and Mineral Cycles
15.1 Sulfur in the Soil Ecosystem
15.2 Biogeochemical Cycling of Sulfur in Soil
15.3 Biological Sulfur Oxidation
15.4 Biological Sulfur Reduction
15.5 Mineralization and Assimilation of Sulfurous Substances
15.6 The Phosphorus Cycle
15.7 Microbially Catalyzed Soil Metal Cycling
15.8 Conclusion
References
16 Soil Microbes
16.1 Foundational Concepts of Bioremediation
16.2 The Microbiology of Bioremediation
16.3 Soil Properties Controlling Bioremediation
16.4 Concluding Observations
References
Concluding Challenge
Index
End User License Agreement
List of Tables
Chapter 1
Table 1.1 Size distribution of soil particle classes
Chapter 4
Table 4.1 Reduction potentials of some common electron acceptors functioning ...
Table 4.2 Some groupings of soil microbes based on their primary energy sourc...
Chapter 7
Table 7.1 Biological interactions occurring in soil ecosystems
Table 7.2 Vitamin‐producing and vitamin‐requiring populations in soil
Chapter 8
Table 8.1 Examples of reports of modification root communities by amendment w...
Table 8.2 Comparison of properties of nonrhizosphere, rhizosphere, and mycorr...
Chapter 11
Table 11.1 Examples of nitrogen distribution in mineral and organic forms: ag...
Table 11.2 Oxidation state of nitrogen compounds associated with soil nitroge...
Table 11.3 Common species of autotrophic nitrifiers, their sources, and morph...
Chapter 12
Table 12.1 Examples of diazotrophs commonly found in soil, rhizosphere, and s...
Chapter 13
Table 13.1 Examples of angiosperm families involved in nitrogen‐fixing actino...
Chapter 15
Table 15.1 Oxidation state of major sulfur compounds in soil
Table 15.2 Metabolic properties of commonly studied
Thiobacillus
species
List of Illustrations
Chapter 1
Figure 1.1 Metal‐impacted site in Palmerton, PA (USA). (a) Site without recl...
Figure 1.2 Subsidence pole located in the Everglades Agricultural Area of So...
Figure 1.3 Designation of soil textural classes by principal mineral compone...
Figure 1.4 Comparison of idealized soil profile models for temperate and tro...
Figure 1.5 Variation of surface area of soil particles: The particles are as...
Figure 1.6 Schematic drawing of divalent metal (M) salt bridge linking of th...
Figure 1.7 Hypothetical data reflecting alteration of apparent pH optima by ...
Figure 1.8 Oxidative coupling of aromatic compounds. Mechanism showing forma...
Figure 1.9 Basic elements of soil substituents contributing to aggregate for...
Chapter 2
Figure 2.1 Outline of a typical ATP analysis procedure for estimating soil m...
Figure 2.2 Outline of aerobic respiration method for estimating soil microbi...
Figure 2.3 Outline of the chloroform fumigation‐incubation procedure for est...
Figure 2.4 Outline of procedure for estimation of microbial biomass using di...
Figure 2.5 Outline of viable plate count method for estimating numbers of or...
Figure 2.6 Outline of most probable number method for estimating number of o...
Figure 2.7 Outline of
polymerase chain reaction
(
PCR
) process for amplifying...
Chapter 4
Figure 4.1 Examples of laboratory‐incubated open and closed systems for stud...
Figure 4.2 Idealized bacterial growth curve.
Figure 4.3 Bacterial growth curve resulting from sequential catabolism of tw...
Figure 4.4 Classical Monod equations describing microbial growth, cell mass ...
Figure 4.5 Glycolytic conversion of glucose to pyruvate. Note the net produc...
Figure 4.6 Production of ATP via transport of electrons through an electron ...
Figure 4.7 The tricarboxylic acid cycle (TCA).
Figure 4.8 General organic matter transformations associated with methanogen...
Figure 4.9 Conceptual model of carbon catabolism by the soil heterotrophic m...
Figure 4.10 Examples of pathways leading to entry of the carbons of aromatic...
Chapter 5
Figure 5.1 Example of variation of an hypothetical biological activity with ...
Figure 5.2 Hypothetical curves describing response of soil biological activi...
Figure 5.3 Variation in aerobic biological activity in soil. In this hypothe...
Figure 5.4 Effect of flooding a dry histosol on aerobic bacterial population...
Figure 5.5 Redox potential and oxygen tension patterns in an hypothetical fl...
Figure 5.6 Typical response of a mesophilic bacterial population to temperat...
Chapter 6
Figure 6.1 Generalized rate curve for an enzyme‐catalyzed reaction where V
ma
...
Figure 6.2 Michaelis–Menton equation and some conversions which are useful i...
Figure 6.3 Use of Eadie–Scatchard plots to distinguish multiple forms of enz...
Figure 6.4 Conceptual model of the distribution of enzymatic activity within...
Chapter 7
Figure 7.1 Survival and growth of
Escherichia coli
in sterile Pahokee muck. ...
Figure 7.2 Adaptations in a generalized microbial community to reestablish c...
Chapter 8
Figure 8.1 Schematic diagram of the physical relationship of primary compone...
Chapter 9
Figure 9.1 A generalized carbon cycle model with biological and atmospheric ...
Figure 9.2 A generalized model of the nitrogen cycle.
Figure 9.3 A model of the soil phosphorus cycle with soil mineral reservoirs...
Figure 9.4 A model of the sulfur cycle showing generalized interactions of b...
Figure 9.5 Examples of the central role of plant biomass in sequestering var...
Figure 9.6 Disassembly of plant organic matter into various primary inorgani...
Figure 9.7 The road from an inorganic existence through biomass and return t...
Chapter 10
Figure 10.1 Conceptual model of carbon cycle with transfers between major so...
Figure 10.2 Structural formulae of cellulose and amylose.
Figure 10.3 Structural formula for
Escherichia coli
peptidoglycan cell wall ...
Figure 10.4 Biphasic decomposition curves for complex organic amendments to ...
Chapter 11
Figure 11.1 Conceptual model of the nitrogen cycle. Nitrogen reservoirs encl...
Figure 11.2 Processes contributing to soil nitrogen balance.
Figure 11.3 Nitrate‐nitrite cycle involving diffusion of nitrate and nitrite...
Chapter 12
Figure 12.1 Major nitrogen inputs and losses contributing to the soil fixed ...
Figure 12.2 Some alternate substrates reduced by the nitrogenase system.
Chapter 13
Figure 13.1 Root nodules formed by
Bradyrhizobium japonicum
and soybeans.
Chapter 14
Figure 14.1 Summary of the electron transport pathway leading from oxidation...
Figure 14.2 Reaction sequence leading to ozone formation and the role of nit...
Figure 14.3 Outline of a most probable number procedure for estimating denit...
Figure 14.4 Outline of a general procedure using the acetylene block method ...
Chapter 15
Figure 15.1 Examples of organic sulfur compounds found in soil.
Figure 15.2 Major features of the sulfur cycle.
Figure 15.3 Major soil phosphorus cycle reservoirs.
Figure 15.4 Primary metal reservoirs in soil.
Figure 15.5 Metal‐contaminated site in Palmerton, PA (USA), showing effect o...
Guide
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Table of Contents
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Soil Microbiology
Third Edition
Robert L. Tate
Department of Environmental Sciences, Rutgers University,New Brunswick, NJ, USA
This third edition first published 2021© 2021 John Wiley & Sons, Inc.
Edition HistoryWiley (1e, 1994); Wiley‐Blackwell (2e, 2000)
All rights reserved. No part of this publication may be reproduced, stored in a retrieval system, or transmitted, in any form or by any means, electronic, mechanical, photocopying, recording or otherwise, except as permitted by law. Advice on how to obtain permission to reuse material from this title is available at http://www.wiley.com/go/permissions.
The right of Robert L. Tate to be identified as the author of this work has been asserted in accordance with law.
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Library of Congress Cataloging‐in‐Publication Data
Names: Tate, Robert L., 1944– author.Title: Soil microbiology / Robert L. Tate, Rutgers University, Department of Environmental Sciences, New Brunswick, NJ.Description: Third edition. | Hoboken : Wiley‐Blackwell, 2020. | Includes bibliographical references and index.Identifiers: LCCN 2020028078 (print) | LCCN 2020028079 (ebook) | ISBN 9780470311103 (cloth) | ISBN 9781119114352 (adobe pdf) | ISBN 9781119114246 (epub)Subjects: LCSH: Soil microbiology.Classification: LCC QR111 .T28 2000 (print) | LCC QR111 (ebook) | DDC 579/.1757–dc23LC record available at https://lccn.loc.gov/2020028078LC ebook record available at https://lccn.loc.gov/2020028079
Cover Design: WileyCover Image: © gehringj/Getty Images
to Ann, Robert, and Geoffrey.
Preface
As I sit at my desk contemplating the appropriate words for this preface to the third edition of Soil Microbiology, a question arose of just why the rather long endeavor of writing another edition was necessary. Certainly, the basic tenets of the discipline are evolving, but not at a rapid rate. The objective of the first edition – “to provide the student with a strong basic knowledge of the biological, physical, and chemical properties of the soil and the microbes contained therein” – is unchanged. What has expanded significantly is our experience in using the concepts of soil microbiology to solve our expanding list of environmental problems. Thus, the most obvious differences between the previous editions and this one is the inclusion of information regarding soil microbial diversity and bioremedation of soil systems. Although the “central dogma” underlying these topics is still evolving, we can now include in a basic textbook the elucidation of the status of the topics and highlighting areas of deficiency in our knowledge base.
When I first began contemplating the task of writing this edition, I asked many of my close associates what they felt was the greatest need of the text (as I did for the second edition). Bioremediation and microbial diversity were frequently mentioned as possible topics but one response stands out in my mind. An individual whose opinion I highly respect strongly stated that no “new words” should be added. Students were already faced with a “mountain of information” to master. I must admit that I too agree, at least in part, with this observation. Students in my own classes commonly are overwhelmed by the vast amount of information before them. It is with this thought in mind that I went ahead and added more “words” to each of the chapters. My goal was to clarify the relationship of soil microbiology concepts to the general environmental matters with which students are experienced and to highlight new endeavors in the area of primary research. Since much of the foundation of soil microbiology derives from agriculturally based studies and our discipline remains a primary support for efficient production of food and fiber, the understanding of the agricultural environment is still a major part of our soil microbiology foundation. However, this foundation is now greatly extended into more general soil concerns, such as urban soil management and soil stewardship and reclamation practices.
Lastly, I have tried to maintain the flavor of the first edition. Students need more than just a presentation of the “facts.” Entries into the world of primary research literature are essential to provide a foundation for careers in our science. Thus, although complete review of the literature is not possible, an attempt was made to highlight a significant mass of current as well as historical research references. My apologies are offered to associates whose publications were overlooked, but such omissions are unavoidable under the page limitations for a basic text and to meet the objective of not overwhelming students with masses of new information. Students are challenged not only to explore the principles provided in Soil Microbiology but also to delve into the rich variety of primary research that has been amassed supporting the principles of soil microbiology and pointing the way to future endeavors.
I take this opportunity to thank my colleagues and students who have provided the inspiration and conducted the research that has made this book possible. In particular, I also thank the current members of my soil microbiology research group who have had to endure my deficiencies in providing true focus to their research endeavors as I put these words to paper. Their patience is gratefully acknowledged and highly appreciated. It is again my hope that this treatise will provide a basis for growth in the science of soil microbiology and an inspiration to the careers of young scientists.
Lastly, I must take the opportunity to thank Dr John Kelly. Our discussions and his contributions to Chapters 2 and 3 were indispensable. As with all of my interactions with John over the decades, he has provided essential insights into the nuances of environmental science.
Robert L. Tate III
New Brunswick, NJ
November 2019
Introduction
Soil microbes have been studied as interesting life forms. They also have been exploited as producers of substances of great societal importance, ranging from food and fiber to a variety of antibiotics. Agricultural‐based research as well as basic research have provided a meaningful demand for monetary support. Today, environmental scientists, regulators, and the lay public are faced with the added demand for answers to microbiological concerns far beyond these basic science and agricultural needs. Examples of the extended informational voids include management of reclamation sites and the reparation of damaged soil systems, be they mismanaged or chemically contaminated.
As recently as the time of publication of the first edition of Soil Microbiology, justification for the primary interest in soil microbiology involved optimization of agricultural production or simply providing a vehicle for study of essential biochemical processes (e.g. DNA, RNA, and other basic biochemical concerns.). Indeed, not only is an appreciation of the biological processes occurring in soil essential to achieve societal goals of caring for terrestrial ecosystems but true wisdom in decision making is predicated on an understanding of how the individual soil biologically based processes combine to produce a vital, sustainable whole. The parts assembled into a viable soil system clearly produce a whole much more dynamic, much greater than can be predicted by their simple summation.
This thesis is underscored by the magnitude and multitude of anthropogenically impacted soil sites currently demanding some form of reclamation management; for example, refuse from energy production or mineral recovery form unsightly slag piles extending across the countryside. From within these piles, a yellow leachate with a pH of nearly 1 frequently flows. Nearly sterile soil and waters result from encounters with this deadly by‐product of resource recovery. The questions become, “How best to prevent the production and leaching of the substances commonly yielded by acid mine drainage? How to restore the impacted soils and waters to functional, esthetic ecosystems? and How can the remains of the mining industry be managed to prevent further environmental degradation?” As will be revealed in the following text, these environmental concerns, although not fully resolved, have been replaced with more demanding concerns associated with climate change induced by basic soil microbially catalyzed by processes.
Another issue, perhaps less dramatic but of similar concern, is the problem of evaluating potential difficulties of amendment of soil systems with genetically engineered microorganisms (gems). The answers appear to be simple. An organic chemical has reached a soil system at toxic concentrations but no microorganisms capable of decomposing the toxicant exist therein. Yet, such microbes can be created in the laboratory through commonly available genetic manipulation procedures. Concerns involve unanticipated ecosystem degradation from the introduction of laboratory‐created, alien organisms into established soil communities. “Will the introduced microbe survive sufficiently long to achieve the objective of its utilization? Will the unique gene carried by this gem be transferred to indigenous organisms, thereby creating an individual with capacity to wreak havoc on an otherwise stable soil system?” These questions represent concerns to which soil microbiologists must respond. Resolution of the conflict requires a clear understanding of the behavior of alien microbes within a functioning soil ecosystem as well as of the dynamics of gene transfer within soil populations.
These initial examples relate to environmental problems whose impact involves the reclamation or management of a limited region of soil. Solutions to environmental problems impacting the totality of our terrestrial system also rely on expansion of our knowledge and databases relating to soil microbial processes. For example, soil is a natural source and sink of greenhouse gases, such as methane, nitrogen oxides, and carbon dioxide. Basically, soil organic matter (humus) resources are the source and sink for these carbon compounds. Furthermore, the quantity of humus retained within a particular soil is the product of the physical, chemical, and biological properties of the system as well as any associated anthropogenic intervention. Therefore, all soil systems are characterized by occurrence of an equilibrium level of soil organic matter.
Anthropogenic intervention into the ecosystem can result in a shift in the quantity of carbon sequestered in the soil. This situation is nowhere more obvious than in soils developed for intensive agricultural production. Historically, the yield of carbon dioxide to the atmosphere due to reduction in the quantity of soil humus in these soils has been significant. Thus, a simplistic means of managing greenhouse gases that could be proposed is to alter the management of soil systems so that they become a sink rather than a source of atmospheric carbon dioxide. An appreciation of the potential benefits of this process can be derived from consideration of variation of soil humus levels resulting from the conversion of intensive cultivation practices into reduced till or no‐till agricultural soil management. Unfortunately, the questions associated with assessing the role of soil in managing greenhouse gases are more complicated. Decisions related to greenhouse gas management and associated terrestrial effects are impacted by, among other factors, the fact that soil temperatures are anticipated to increase due to global climate changes associated with the greenhouse phenomenon. Now an interaction of human soil management decisions, changes in the chemistry of plant inputs due to alteration of plant biomass composition by the elevated atmospheric temperatures, and alteration of soil physical properties (e.g. temperature and moisture) acting together create soil microbial community dynamics that are not as easily forecasted as was possible with alteration of agricultural soil management. An expanded comprehension of soil microbial dynamics and the effect of total‐ecosystem processes on soil biological processes is needed.
It is with these concerns in mind that this treatise is presented. The overall goal is to provide the reader with a strong basic knowledge of the biological, physical, and chemical properties of soil and the microbial community therein necessary to provide the basis for sound environmental management and stewardship decisions.
1Soil Ecosystems: Physical and Chemical Boundaries
Life in soil (e.g. active and resting of microbial species and its distribution within the soil matrix) is the product of direct and indirect interactions between highly variable physical and chemical matrices with associated equally variable biological communities composed of essentially all life forms. Soil biological communities are sustained across an intriguingly interesting span of chemical and physical conditions, especially when compared with the variability of the comparable properties of the environment supporting humans. Unfortunately for the scientists seeking a clear and accurate understanding of the identity and functions of soil microbes, the distribution of the microbes within the soil physical structure is not necessarily readily accessible. The location in soil most important for the function of soil microbes is not the macrosystem clearly accessible for scientific study but rather the microbial community which is impacted most by the properties of the microsites of a few cubic microns wherein they occur and function. Therefore, the primary goal of this introductory chapter of Soil Microbiology is to examine the general properties of soil and their impact on the associated microbial activity. To gain an appreciation of the complexity of the soil microbe's habitat, the overall physical and chemical properties of soil particulates controlling the development of soil communities will be introduced first.
Defining the world of the soil microbes: Microbes can clearly be studied in isolation from their native habitat, i.e. in soil samples of limited size or pure cultures of soil microbes incubated in the laboratory. Indeed, there is much still to be learned by such studies, but a full appreciation of microbes and their contributions to the sustainability of ecosystems can only be fully gained, or perhaps appreciated, by examining their capacity to function within their native habitat. Thus, we must initiate our examination of microbes in soil systems with a consideration of the basic properties of the soil environment itself. As will be demonstrated by the topics presented in this text, life is difficult for the microorganisms growing within the microsites comprising their soil habitat – thereby making “life” for the microbiologist attempting to understand the soil microbial community just as difficult, if not more.
Developing a clear understanding of the dynamics of soil microbial communities presents a formidable practical and conceptual challenge. The practical challenge is that due to the nature of soil itself, most of our endeavors to study the soil microbes must be conducted in the laboratory under less than natural conditions. The conceptual challenge results from the fact that many of the assumptions that we would make regarding the properties of that portion of the soil where the microbe grows are false. We see the general properties of a soil system such as a soil with a plentiful oxygen supply, a near neutral pH, and optimal moisture when in reality the microbes may be actually growing in a vastly different situation, perhaps in an acidic environment, in the absence of molecular oxygen, under water‐limited conditions (e.g. arid or flooded soil). We, the observers, see the macro‐world that we inhabit – the microbe functions within and is controlled by a few cubic micrometers of our world. Thus, the concept of the soil properties controlling microbial development and function can be, and most certainly are, vastly different from our picture of the soil system.
The soil ecosystem is the product of intricate interactions between a physical and chemical matrix of highly variable composition and biological communities composed of essentially all life forms. It is probably realistic to assume that a reasonable understanding of the extreme variability of microsites within the soil is a more modern development. Thus, a first task in studying soil microbial community development and function in soil systems is to expand our concept of the limits of physical and chemical conditions within which microbial life can exist. Thus, it is necessary to consider that the properties of the microbial world are variable within a range that extends far beyond that which is comfortable for us. Microbial life is sustainable across nearly the entire range of chemical and physical conditions existent on planet Earth.
A further limitation impacting the validity of our picture of how microbes function in soil is the fact that most of the data we have collected that is descriptive of their function are derived from laboratory‐based studies examining individual microbial species or strains. Our ability to study the microbes directly in their “home” is limited at best. This simplification of soil physical, chemical, or biological properties, from several to perhaps a single function, has allowed for a reduction in the complexity of the system of study and of data interpretation. But at what cost – reduced understanding of the real functional complexity of the community? In part, to circumvent this limitation, more recently, use of consortia of bacteria and/or fungi for study of more complex processes, such as decomposition of xenobiotic compounds or changes in the diversity of the microbial community, has become the norm. These latter cultures exhibit some of the more complex interactions reflective of the soil ecosystem. Use of defined cultures or even the simple mixtures of microbes making up consortia is generally justified by the conclusion that it is necessary to attain maximum control of experimental variables in order to elucidate clearly the processes of interest.
As an appreciation of the complexities of soils and their microbial populations is developed, the inadequacy of experiments using axenic cultures (that is, cultures composed of a single species or strain of soil microbes) or mixed cultures composed of a small number of microbial strains (that is, a consortia of soil microbes) to evaluate the world of the soil microbes becomes obvious. Generally, the basic properties of the biological processes measured in laboratory culture defy extrapolation to the more complex soil environment. Not only are stresses of the native soil system unmatched with defined culture conditions, but the microbes themselves change phenotypically and even genotypically in response to the laboratory growth conditions. Although the microbes studied may have been isolated from a sample of a soil, their metabolic capabilities and capacity to respond to their physical and chemical environment, as well as the presence of other microbes, may differ meaningfully from the strains existent in the original soil sample. That is, a microbial variant with appropriate properties for optimal growth in test tubes is usually selected either spontaneously (as a result of laboratory culture methods) or through genetic manipulation of the microbial isolates. The former selection results from the rich genetic variations within the genome of each individual bacterial species. It is easy conceptually to assume that each bacterial species present in soil consists of a group of individuals with essentially identical genomes. This viewpoint is far from reality. Bacterial species have similar traits and genetic composition, but their genomes contain many genetic variations (mutations).
Therefore, when members of a previously soil‐resident bacterial species are selected for culture in the laboratory, mutant strains that previously existed in soil as a minuscule portion of the soil population of the species may be better able to grow under the laboratory conditions of the test tube than is the majority strain occurring in the soil community. Thus, a genetic variant becomes the dominant strain studied in the laboratory. Further selection of spontaneously occurring variants may – or more likely does – occur in the laboratory culture. As a result, data collected from experiments with isolated microbial species or strains frequently only explain or mimic the processes occurring in soil in part. Therefore, it is reasonable to conclude that soil microbiologists must expand the purview of experimental design to include the complexities – controllable and otherwise – of the total soil ecosystem. Therefore, the realm of soil microbiology must be defined to include both an understanding of the properties of the microbes themselves along with an appreciation of the impact of variability of the soil environment on these traits. Soil microbial ecology must involve an evaluation of the behavior of organisms in their native habitats. Even the simplification of microbial community dynamics to those of a simple consortium is problematic, when we understand that the microbes growing in soil, rather than functioning within a colony or even a micro‐colony, are more likely part of a biofilm that consists of several species or strains of bacteria with a variety of metabolic or physiological capabilities.
Are soil microbes really that important? To the purist, elucidation of the principles of soil microbiology is immensely interesting and fully justified strictly by the information generated relating to the basic ecological interactions occurring in soil systems. Just the fact that a single gram of soil can contain thousands of different microbial species is sufficient to pique our interest. Yet, due to societal management of terrestrial ecosystems, our concern for soil biological processes reaches far beyond just the realm of basic science. For example, from the world of environmental science, our myopic exploitation of natural ecosystems has resulted in situations where the functioning of resident microbial populations is precluded or severely limited by mismanagement. Spills of toxic organic chemicals result in scarred landscapes. Similarly, products of metal processing have resulted in sites resembling moonscapes (Figure 1.1a). Reclamation of such sites is attempted (e.g. Figure 1.1b), but for attainment of such objectives, management plans must be developed that allow for establishment of essential soil biological processes in soils containing extreme levels of toxic metals or a variety of organic toxicants. For the soils adjacent to a zinc smelter, attainment of improved microbial function required amendment of the soil with an organic matter source (sewage biosolids), liming the soil to raise the soil pH to above 7.0 (to immobilize the toxic metals), and planting the soil with a strain of grass that is capable of growing in soils with elevated metals loadings in order to stabilize the soil on the mountain slopes and reduce the soil erosion. Actually, the contributions of the grass to the microbial function extend far beyond just stabilizing the physical environment. By converting solar energy to plant biomass (photosynthesis), the plants provide the primary microbial energy source for the soil microbes.
In comparison with these obviously detrimental situations, development of soils for agricultural production may also reduce overall soil quality. Tillage initiates processes that may eventually reduce productivity of the soils. Loss of desirable soil structure and reduction of soil organic matter reserves are generally associated with implementation of intensive agricultural practices. Destruction of soil structure increases the bioavailability of native soil organic matter, a major microbial carbon and energy source. Conversion of the soil organic carbon to carbon dioxide reduces the soil productivity and sustainability, thereby reducing soil quality and increasing the production of a greenhouse gas.
A dramatic example of augmented soil organic matter decomposition due to cultivation of a previously undisturbed soil system is provided by observation of changes in soil properties resulting from cropping of peats. Development of these soils for agriculture initially required draining the water, resulting in conversion of the anoxic conditions to an aerobic state. This conversion of the generally anoxic swampy soil to one where molecular oxygen is no longer limiting resulted in stimulation of the aerobic heterotrophic bacteria. The microbes oxidized the plant debris that was accumulated under the swampy conditions prior to site drainage to carbon dioxide, mineral nutrients (e.g. mineral phosphorus and nitrogen), and water, resulting in loss of soil mass. The loss of the organic matter resulted in subsidence of the soil surface (Figure 1.2).
Figure 1.1 Metal‐impacted site in Palmerton, PA (USA). (a) Site without reclamation management. (b) Site following amendment of soil surface with a mixture of sludge, fly ash, lime, and grass seed.
Figure 1.2 Subsidence pole located in the Everglades Agricultural Area of South Florida (USA) showing loss of soil elevation between 1924 and 1979.
In each of these examples – contamination of soil with metals, agricultural cultivation of the soil, or draining of swamps for agricultural production – the physical structure of the soil, its chemical properties, and the function of the biological community have been altered in a manner that reduces the quality of the soil system. Soil is a renewable resource, but the time frame for restoration of a badly damaged soil system may extend over several decades or even centuries. Thus, in the short run, soil must be managed with the philosophy that it is an exhaustible resource.
Proper soil stewardship cannot be achieved without a full appreciation of soil microbiological processes, for the totality of existence of a soil ecosystem relies upon sustaining a functional soil microbial community. To develop appropriate management plans for restoration of damaged systems or for maintenance of ecosystem productivity, a clear understanding of in situ biological processes is necessary. This cannot be fully accomplished by using data generated from the observation of bacterial populations growing at an unnatural rate under the optimized conditions of the laboratory culture flask. Realistic estimates of metabolic activity and the kinetics of the process in the microbe's native environment must be developed. Procedures necessary for maintenance of the soil chemical and physical factors controlling expression of microbial activity in a balanced state are needed to ensure the long‐term survival of critical populations for ecosystem remediation and sustainability. Such factors as temperature, pH, moisture, surface area, osmotic strength, and presence of predators all interact to select for the development and survival of a stable microbial community necessary for long‐term ecosystem function.
The challenge: Once it is understood that reality for soil microbes exists in their natural habitat, the primary challenge becomes defining that habitat. For the soil microbiologist, this is not an easy task. Microbes flourish in temperature‐limited, native systems, under such extreme conditions as experienced in hot spring‐impacted soils or in the cold desert soils of Antarctica. Highly productive soils may become biologically impoverished due to the impact of anthropogenically produced situations, such as those resulting from acid mine drainage or spills of xenobiotic organic compounds. Thus, it becomes clear that the soil ecosystem can be spoken of in general terms, but a true encounter with soil ecology must include an assessment of the length and breadth of these highly variable systems.
This assessment must start with differentiation of the entity to be studied. Soil microbiologists must realize that they are studying specific soil types, not simply “soil.” The commonly heard statement among soil microbiologists, “Soil was used in our experiments,” would sound as strange to a soil scientist as would “A bacterium was studied” would to a biologist. Currently, the US soil classification system divides world soils into 12 orders (based on soil properties that reflect soil development). Examples of soil orders are aridisols (dry soils), andisols (volcanic soils), gelisols (permafrost‐impacted soils), histosols (organic soils), inceptisols (embrionic soils), spodosols (typical of forest systems), and vertisols (characterized by soils with high‐swelling clay contents). These orders are subdivided into suborders, great groups, subgroups, families, and series. Currently, over 15 000 soil series have been identified. (See Brady and Weil 2017 for further discussion of soil taxonomy.) This situation of defining the specific soil unit of study is further complicated by the fact that a given field site may contain one or more soil series. Furthermore, biological activity within the same soil series varies with such ecosystem depending on properties as plant type and distribution, seasonal climatic variation, and management practices – current and historic. Yet, the properties of the soil type underlying an ecosystem as defined and impacted by the aboveground communities must be assessed and understood.
1.1 Soil as an Ecosystem
The properties of a soil system are not simply a summation of the general properties of its individual physical, biological, and chemical components. They are the result of the individual properties as modified by their interaction with each other as well as their distribution within the soil matrix. These interactions result in a soil ecosystem that is truly much greater than just the sum of its parts. For example, association of the soil mineral and organic materials in soil aggregates results in co‐occurrence of anoxic and aerobic biological processes within a few millimeters or less of each other in the surface horizon of a soil permeated by our oxygen atmosphere. As will be elucidated in Chapter 2, even limited growth of a pioneer population of microbial cells can result in modification of the microbe's environment sufficiently to enhance future growth and community development. Thus, a soil ecosystem could be said to be evolving toward an optimized ecological state dictated by the interactions of each of the soil components.
Therefore, any analysis of the structure of soil systems and the principles describing their function must commence with an evaluation of (i) the soil physical components, (ii) their assembly into the physical whole, and (iii) the implications of this structure on soil biological processes. The study must then proceed to a determination of the feedback mechanisms involved with living populations interacting with their physical environment. This analysis is necessary to develop fully the principles or maxims describing microbial interactions in soil and their importance to that portion of the system most commonly regarded esthetically – the aboveground plant and animal community.
1.1.1 Soil System Function
A soil's classification could be based on an understanding of the applicable physical, chemical, and biological properties of soil that make each soil unique. For example, soil definition could be based on our understanding of the impacts of plant community development on soil ecosystem properties whereas others studying the soil system could emphasize the variation in general soil properties, emphasizing an appreciation of the foundational role of soils in societal development, function, and sustainability. Indeed, societies can rise and fall based on the capability of their soil to provide ecosystem services (French 2010). Since soil microbes are key participants in the provision of these services, societies are truly built upon the function, sustainability, and diversity of the soil microbial community. To fully appreciate the intricacy of this soil microbial community, our more general image of the material that we walk on, build our infrastructure on and depend upon for food and fiber production must be enlarged to include a picture of the microscopic world in which soil microorganisms live and function.
The soil physical structure and soil microbes: Most soils are classified as mineral soils – that is, soils that are composed primarily of mineral matter and whose physical properties are controlled by the proportions of the mineral particulates contained therein. These soils generally contain from less than 1% to approximately 4% organic matter, but they may consist of as much as 20% soil organic matter. Additionally, an organic layer up to 30 cm in depth may be found on the soil surface (e.g. a forest litter layer). These soils are to be contrasted with the much less commonly encountered organic soils (histosols). Organic soils contain more than 20% organic matter as exemplified by peats and mucks.
The most obvious components of mineral soils are sand, silt, and clay, each of which is defined by its physical dimensions (Table 1.1). Note that this separation of soil particles is based on particle size only. For example, the clay fraction is strictly defined as having a mean diameter of less than 2 μm. Therefore, this fraction will contain clay minerals plus other soil components, which are not necessarily clay minerals but are of comparable size. A soil is classified into a specific textural category by the quantities of the mineral separates that it contains (Figure 1.3)
Table 1.1 Size distribution of soil particle classes
Source: USDA Public Domain.
Particle class
Subclass
Mean diameter (mm)
Sand
Very coarse sand
2.00–1.0
Coarse sand
1.0–0.5
Medium sand
0.5–0.25
Fine sand
0.25–0.1
Very fine sand
0.1–0.05
Silt
0.05–0.002
Clay
<0.002
This disposition of soil by textural classification is useful for characterizing a particular soil of interest (either for field or laboratory experiments), but it is in reality the soil structure – that is, how these individual components are assembled – that best defines the habitats of soil microorganisms. Two soils may have nearly identical textural compositions yet exhibit extremely contrasting microbial activities. For example, microbial properties of a silt loam in an area flooded with acid mine drainage waters would reflect the prevailing stresses of oxygen deprivation and extremes of acidity, whereas a silt loam from a well‐maintained agricultural site would be free of such limitations. Furthermore, a soil with a well‐developed aggregate structure in contrast to one where the structure has been lost due to intensive cultivation would be more conducive to microbial community development.
Clearly, a soil classification system is required that is descriptive of in situ ecological influences on biological properties. This information is provided by soil classification systems, such as those of the United States Department of Agriculture (USDA) or the Food and Agriculture Organization of the United Nations (FAO). Within these taxonomic systems, soils are grouped by field and laboratory properties, among which are soil texture, moisture, pH, temperature regimes, and horizon development.
Soil profile development: An appreciation of soil horizon development and its effect on soil microbial activity is necessary to develop a more complete picture of the impact of soil biological processes on the properties of an ecosystem. A soil horizon is a layer of soil approximately parallel to the land surface and differing from adjacent layers physically, chemically, and biologically, or in characteristics such as color, structure, texture, consistency, biotic populations, and pH. Soil horizonal development is clearly a product of current ecosystem properties as well as of site history. Each soil subgroup description includes an analysis of horizonal structure. Microbiological properties of a specific horizon may be studied in isolation from other portions of the soil profile. In such studies, the designated portion of the soil profile may be defined as an ecosystem in itself.
Figure 1.3 Designation of soil textural classes by principal mineral component analysis.
Source: USDA Public Domain.
The most commonly studied of soil horizons in microbiological research are the O, A, and B horizons, although as a result of complications of groundwater pollution, considerable research effort is being expended to understand biological processes occurring in deeper‐lying aquifer materials. O horizons are dominated by organic material and are exemplified by forest litter layers. The A horizons are mineral layers formed on the soil surface or below the O horizon. These regions are characterized by accumulations of organic materials intimately associated with soil mineral matter. In many situations, these organic materials are a product of plant community development in native, unmanaged ecosystems. A horizons are usually spoken of as surface soils. Colloidal organic matter concentrations tend to be maximized in this portion of the mineral soil profile. B horizons are usually formed below an O or A horizon and are dominated by (i) carbonates, gypsum, or silica, alone or in combination; (ii) evidence of removal of carbonates; (iii) concentrations of sesquioxides; (iv) alterations that form silicate clay; (v) formation of granular, blocky, or prismatic structure; or (vi) combinations of these. In soils without organic surface accumulations, microbial activity tends to be maximized in the A horizon and declines precipitously in the B horizon.
1.1.2 Soil Formation and the Microbial Community
Soil microbiologists frequently report results of study of a limited number ofsoil types and provide minimal descriptions of the sites from which the soil samples were collected. It is not unusual to see statements such as “a garden soil was used” in the literature. From the foregoing discussion, it is apparent that an understanding of not only the currently existing physical and chemical properties of the soil but human‐imposed as well as natural events influencing soil formation must be examined. Furthermore, primary goals of research include not only improvement of our understanding of the function of the local soil site but also elucidation of the soil science principles that will increase our understanding of soils in general. Indicating the ecosystem type from which a particular soil sample was collected is generally inadequate to allow proper interpretation of the data, extrapolation of the principles revealed by the research, and, frequently, replication of the study by other researchers asking similar scientific questions. Although it may seem adequate to report that a grassland soil was evaluated in a particular experiment, application of proper soil classification procedures may reveal that a variety of soil types occur within the region classified by an ecologist as a grassland. That is, to conduct a meaningful examination of a soil ecosystem, the area to be sampled must be appropriately described. An appreciation of the variation of soil properties and the importance of the variation to the ecosystem services provided by the soil microbes can be gained by a short consideration of the controllers of soil genesis.
State Factor Theory of soil development: The effects of interactions of total ecosystem properties on soil development were described succinctly by Jenny (1941) in his State Factor Theory, frequently referred to as the CLORPT model. The original model stated that soil development is a function of climate, organisms, relief (topography), parent material, and time. The theory was subsequently modified to include human influences (Amundson and Jenny 1991). Although the model emphasizes the major factors affecting soil formation, possibly primarily from a macro‐environment view, it is reasonably clear that each of the factors affects and is affected by the soil microbial community. The synergistic associations of soil microbes and their physical and chemical environment determine the properties of all soils involved as well as the ecosystem services derived from the soil. The effect of some of the factors, such as climate, on soil microbes is clear, especially when comparing such extremes as desert and forest ecosystems or even boreal and tropical rainforests, whereas others such as relief are less obvious. Perhaps the latter effects on microbial function could be clarified by consideration of variation of temperature and moisture on east versus west aspects of a hill, where soil temperature would vary due to different impacts of morning and afternoon sun exposure or direction of prevailing rain storms.
In regard to human impacts on soil formation, at one point in human history agriculture could have been considered to be the primary controller of soil development (e.g. destruction of soil structure, alteration of nature and properties of organic matter inputs) but now it is reasonably easy to accept the observation that the genesis of all soils is directly affected by human society (e.g. distribution of pollutants, variation in air and water contents, as well as alteration of climate via anthropogenic‐imposed climate change or even drainage of large swamps). In all cases, the dynamics and nature of the soil microbial community are determined at least in part by the evolving soil properties as much as the evolution of the soil properties are determined by the function of the soil microbial community.
Interrelationship of microbial communities throughout the soil profile: A complication to description of soil systems results from the fact that soils are continually changing. To the casual observer, it may seem that soil types and their properties represent a constant in their conceptualization of an ecosystem. In reality, as can be concluded from the CLORPT model, soil physical, chemical, and biological properties are continually changing. Soil pH, salinity, aggregate structure, and cation exchange capacity are but a few examples of soil properties constantly evolving due to the actions of the biological community (plant, animal, and microbes). For example, microbes produce organic acids, carbon dioxide, and hydrogen ions that alter the soil pH, thereby affecting the solubilization of soil minerals and ultimately the salinity of soil water. Additionally, as a result of variation in the composition and production of root exudates, aboveground differences in plant community type and density can cause variations in belowground microbial and enzymological activities that may range over several orders of magnitude. This effect of plant biomass productivity on soil enzymes is exemplified through analysis of enzyme activity in a reasonably uniform organic soil (i.e. a single soil type) in the Everglades Agricultural Area (South Florida, USA). Acid phosphatase, invertase, xylanase, cellulase, and amylase activities varied by as much as 50‐fold between not‐cultivated and soils cultivated to sugarcane, St Augustinegrass (Stenatophrum secundatum [Walt] Ktze.), or paragrass (Brachiaria mutica [Forsk.] Stapf) (Duxbury and Tate 1981). A limited understanding of the complexities of these organic soil‐based systems would result if each soil sample (uncultivated or from grass or sugarcane fields) were simply classified as agricultural soil. Inputs from the aboveground plant community necessitate dividing the study area into at least three ecosystem types. Note also that in the study cited, all aboveground biomass could have been grouped into a category of grasslands (i.e. both sugarcane and the St Augustinegrass are by definition grasses).
Although plant communities are instrumental in soil development, it must be stressed that soil properties can be very different in seemingly related ecosystem types. This situation is exemplified by comparing two large forest groupings: temperate and tropical forest soils. Temperate forest soils may be moderately acidic (pH 3.5–4.5) and possess a well‐defined horizonal development (Figure 1.4). They may also have a surface litter layer plus a subsurface horizon (spodic horizon) with an accumulation of organic matter. Clearing of forests and cultivation of such soils in the temperature regions has resulted in moderately productive agricultural systems. In contrast, tropical rainforest soils generally lack a surface organic horizon; are usually highly acidic, nutrient‐poor soils; and can be poor candidates for agricultural development.
Figure 1.4 Comparison of idealized soil profile models for temperate and tropical forest soils. (a) Spodosol surface horizons with accumulated organic matter, and leached A horizon. Spodosols are exemplified by acidic forest soils. (b) Latosilization as would be seen in an oxidol (tropical forest ecosystem). These soils are generally highly leached, acidic soils with no significant humus layer. See Fanning and Fanning (1989) for further discussion of these soil types.
