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Soil 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...