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
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.